diff --git a/about/code_of_conduct/index.html b/about/code_of_conduct/index.html deleted file mode 100644 index 700dbbd..0000000 --- a/about/code_of_conduct/index.html +++ /dev/null @@ -1,17 +0,0 @@ - - -

Code of Conduct

Our Pledge

We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.

We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.

Our Standards

Examples of behavior that contributes to a positive environment for our community include:

  • Demonstrating empathy and kindness toward other people
  • Being respectful of differing opinions, viewpoints, and experiences
  • Giving and gracefully accepting constructive feedback
  • Accepting responsibility and apologizing to those affected by our mistakes, -and learning from the experience
  • Focusing on what is best not just for us as individuals, but for the overall -community

Examples of unacceptable behavior include:

  • The use of sexualized language or imagery, and sexual attention or advances of any kind
  • Trolling, insulting or derogatory comments, and personal or political attacks
  • Public or private harassment
  • Publishing others’ private information, such as a physical or email address, without their explicit permission
  • Other conduct which could reasonably be considered inappropriate in a professional setting

Enforcement Responsibilities

Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.

Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.

Scope

This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.

Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at -steering-council@scverse.org. -All complaints will be reviewed and investigated promptly and fairly.

All community leaders are obligated to respect the privacy and security of the reporter of any incident.

Enforcement Guidelines

Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:

1. Correction

Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.

Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. -A public apology may be requested.

2. Warning

Community Impact: A violation through a single incident or series of actions.

Consequence: A warning with consequences for continued behavior. -No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. -This includes avoiding interactions in community spaces as well as external channels like social media. -Violating these terms may lead to a temporary or permanent ban.

3. Temporary Ban

Community Impact: A serious violation of community standards, including sustained inappropriate behavior.

Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. -No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban.

4. Permanent Ban

Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.

Consequence: A permanent ban from any sort of public interaction within the community.

Attribution

This Code of Conduct is adapted from the Contributor Covenant, version 2.1, available at https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.

For answers to common questions about this code of conduct, see the FAQ at https://www.contributor-covenant.org/faq. -Translations are available at https://www.contributor-covenant.org/translations.

\ No newline at end of file diff --git a/about/index.html b/about/index.html deleted file mode 100644 index 918dd80..0000000 --- a/about/index.html +++ /dev/null @@ -1,8 +0,0 @@ -About scverse - -

About scverse

scverse is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.

Check out our introductory blog post and mission statement for more details.

Sponsorship

scverse is a fiscally sponsored project of NumFOCUS, a nonprofit dedicated to supporting the open-source scientific computing community. -If you like scverse and want to support our mission, please consider making a donation to support our efforts.

NumFOCUS is a 501(c)(3) non-profit charity in the United States; as such, donations to -NumFOCUS are tax-deductible as allowed by law. As with any donation, you should -consult with your personal tax adviser or the IRS about your particular tax situation.

\ No newline at end of file diff --git a/about/mission/index.html b/about/mission/index.html deleted file mode 100644 index 496e2d9..0000000 --- a/about/mission/index.html +++ /dev/null @@ -1,10 +0,0 @@ - - -

Mission Statement

Goals

We want to make analysis tools for omics data in the life sciences as accessible as possible. This means:

  • Interoperability – we focus on developing open, standardized, and efficient file formats to encourage data sharing and re-use.
  • Diversity – we believe in removing barriers to participation in research, including economic factors and institutional culture. Our tools will have the most impact if they are developed by and for a diverse community.
  • Transparency – we do our work as openly as possible and welcome our community to join the decision making process.
  • Simplicity – invent as little as possible and work with standard pydata types. We strive for easy-to-use interfaces that reduce mental overhead.
  • Efficiency – our tools should require as little computational resources as possible. This makes analysis of large datasets more accessible, and makes cutting edge research possible.

Organization and vision

The growing adoption of Python for single-cell omics data analysis has been catalyzed by Scanpy and AnnData. -Around this infrastructure an ecosystem of packages has been created by various developers and institutions — extending single-cell analysis to different modalities and addressing challenges at the cutting-edge of single-cell research. We believe that progress in this field can’t be silo’d to a few groups. To further nurture the growth of this ecosystem, we’ve formed a new organization – scverse.

scverse is a consortium of tools with users and developers across the world. To sustain the utility and growth of the ecosystem, it’s essential that the core analytic tools are robust and well-maintained. This entails consistent support and improvement of tools beyond what’s possible in the conventional single-lab academic setting.

scverse provides high quality infrastructure for analysis of single cell omics data. These core tools are well documented, tested, and provide broad functionality. They work with standardized data structures which use common Python numeric types and have interchange-friendly on-disk formats.

We define core tools as those which facilitate sharing data through common formats, or provide foundational support for single cell datatypes (e.g. modality-specific IO, toolkits) and analyses. -These tools are placed under shared maintenance and development in the scverse GitHub organization.

scverse core tools are expected to interface with and be supplemented by other tools in the ecosystem. scverse strives for synergy and interoperability with the ecosystem of packages built around these core tools, to ultimately provide users to cutting-edge and varied selection of analysis methods.

User engagement

We are community-driven and committed to keeping the scverse community open. We strive to actively foster a community where everyone is and feels welcomed, and where there are no barriers to contributions in any form. We welcome newcomers and pledge to build an environment where they can grow as contributors, developers and community members. Together with technical and development support, we also support our users through:

  • Clear documentation of code and usage via docs and tutorials.
  • Participation in development through issues and pull requests.
  • Community forums, such as our Discourse, Zulip, and Twitter.
  • Workshops at which we teach analysis workflows based on the scverse ecosystem.

Developer engagement

Tools within scverse are deliberately not unified under a single package, and instead form a consortium of core analytic tools with shared maintenance responsibilities. -Development of these packages is not restricted – contributions are welcomed and publicly acknowledged. -However, scverse aims to support the external development of new approaches to analyze and work with single cell data. -We encourage the creation of new methods and tools on top of the core packages and data-structures.

We support the development these ecosystem packages by:

  • Providing stable APIs to build on top of.
  • Providing standardized and well supported data structure to pass around data.
  • Making sure all contributions are recognized in our change logs and documentation.
  • Promoting 3rd party packages that rely on scverse via our websites and social media feeds.
  • Establishing open communication channels for:
    • Discussion and collaboration between developers.
    • A common forum for user support and engagement.
\ No newline at end of file diff --git a/about/roles/index.html b/about/roles/index.html deleted file mode 100644 index 5d9d6c6..0000000 --- a/about/roles/index.html +++ /dev/null @@ -1,36 +0,0 @@ - - -

Roles And Responsibilities

The purpose of this document is to formalize the governance process used by the scverse project, to clarify how decisions are made and how the various groups within our community interact.

As a whole, we are a consensus-based community project. -However, any subproject within the scverse can have their own governance system as long as they do not conflict with the rules set out here. -Anyone with an interest in the project can join the community, contribute to the project design, and participate in the decision making process. -This document describes how that participation takes place, how to find consensus, and how deadlocks are resolved.

The Community

The scverse community consists of anyone using or working with the project in any way.

Contributors

A community member can become a contributor by interacting directly with the project in concrete ways, such as:

  • proposing, discussing, or reviewing a change to the code, documentation, or specification via a GitHub pull request to any https://github.com/scverse repository;
  • reporting a GitHub issue to any https://github.com/scverse repository;
  • discussing examples or usage issues on any of our discussion platforms

among other possibilities. -Any community member can become a contributor, and all are encouraged to do so. -By contributing to the project, community members can directly help to shape its future.

All community members are required to adhere by our code of conduct. -Potential contributors are encouraged to read the Contributing Guide.

A community member becomes a contributor when the following criteria are met:

  • At least two core team members support their addition
  • The new member has supported the project several times, either through code or otherwise

Project developers

Individual projects within scverse have a lot of freedom in deciding how their projects are developed. -This includes who gets commit rights to their projects.

Core team

The core team are community members that have demonstrated continued commitment to the project through ongoing contributions. -They have shown they can be trusted to maintain scverse with care. -Team members appear as organization members on the scverse GitHub organization and are on our @scverse/core GitHub team.

There are sub-roles within the core team depending on the kinds covering different kinds of contributions and responsibilities.

Core developers

Core developers are members of the core team who have made signifigant code contributions to scverse. -They are granted additional rights so they can more easily carry on with their scverse related activities. -These rights include: merging approved pull requests, voting for and against contested pull-requests, and being involved in deciding major changes to the API. -Core developers are on our @scverse/core-devs GitHub team.

All core packages must have at least one core developer as a maintainer. -New core developers can be nominated by any existing core developer. -While there is no hard-and-fast rule about who can be nominated, ideally, they should have:

  • Been part of the community for a significant amount of time
  • Contributed significant changes of their own
  • Contributed to the discussion and review of others’ work
  • Collaborated in a way befitting our community values

After nomination admission will be decided by two-thirds majority vote on a private mailing list by the core team.

Primary maintainers of new core packages, who are not already core developers, will be invited to join.

Steering Council

The Steering Council (SC) members are core team members who have additional responsibilities to ensure the smooth running of the project. -SC members are expected to participate in strategic planning, approve changes to the governance model, and make decisions about funding granted to scverse itself (funding to community members is theirs to pursue and manage). Changes that impact the full project require analysis informed by extensive experience with both the project and the larger ecosystem. -When the core team (including the SC members) fails to reach a consensus in a reasonable timeframe, the SC is the entity that resolves the issue.

Members of the steering council also have the “owner” role within the scverse GitHub organization -and are ultimately responsible for managing the scverse GitHub account, the @scverse -twitter account, the scverse website, and other similar scverse-owned resources.

The steering council is currently fixed in size to three members. -This number will be increased as our community grows and diversifies, but will always be an odd number to ensure a simple majority vote outcome is always possible. -The initial steering council of the scverse consists of

The SC membership is revisited every January. -SC members who do not actively engage with the SC duties are expected to resign. -New members are added by nomination by a core developer. -Nominees should have demonstrated long-term, continued commitment to the project and its mission and values. -A nomination will result in discussion that cannot take more than a month and then admission to the SC by consensus. -During that time deadlocked votes of the SC will be postponed until the new member has joined and another vote can be held.

The scverse steering council may be contacted at steering-council@scverse.org, or via the @scverse/steering-council GitHub team.

Management committee

The management committee consists of PIs that support the development of scverse core projects. Members of the management committee are expected to secure funding and allocate resources to the continuous development of one or more core projects.

PIs supervising the development of new core packages, who are not already part of the managment committee, will be invited to join.

Scientific advisory board

The scientific advisory boards consists of highly experienced scientists devoted to research in single cell omics analysis. In an annual meeting, the scientific advisory boards assesses the progress of scverse and suggests priorities for the next year based on the latests developments in the field.

Members of the scientific adivsory boards are nominated by the core team.

Decision Making Process

Decisions about the future of the project are made through discussion with members of the community. -All non-sensitive project management discussion takes place on the issue trackers of the https://github.com/scverse repositories, in public channels of our chat, or on the forums. -Occasionally, sensitive discussion may occur via a private message.

Decisions should be made in accordance with the mission and values of the scverse project.

scverse uses a “consensus seeking” process for making decisions. -The group tries to find a resolution that has no open objections among relevant core team members. -Core members are expected to distinguish between fundamental objections to a proposal and minor perceived flaws that they can live with, and not hold up the decision-making process for the latter. -If no option can be found without objections, the decision is escalated to the SC, which will itself use consensus seeking to come to a resolution. -In the unlikely event that there is still a deadlock, the proposal will move forward if it has the support of a simple majority of the SC.

If an objection is raised on a lazy consensus, the proposer can appeal to the community and core developers and the change can be approved or rejected by escalating to the SC.

\ No newline at end of file diff --git a/blog/hello-world/index.html b/blog/hello-world/index.html deleted file mode 100644 index 474b41c..0000000 --- a/blog/hello-world/index.html +++ /dev/null @@ -1,22 +0,0 @@ -Hello world - -

Hello world

May 17, 2022

Due to the increasing reliance of scientific research on complex computational pipelines, foundational software in the life sciences has outgrown individual labs and institutes in terms of its scale and impact. -This has motivated us to start something more than a code repository for an exciting new project – a new consortium to organize and support core (mostly) Python tools for single cell life science research. -We are excited to announce scverse.

What tools are part of scverse?

Our primary experience lies in the field of computational biology with an emphasis on single-cell omics technologies. This experience has defined our initial scope and focus in the very beginning of our journey. Hence, we start with two key data structures for single-cell data in the Python ecosystem, AnnData for uni-modal data and MuData for multi-modal data, together with Scanpy for general purpose single-cell analysis, muon for multimodal single-cell analysis, scvi-tools for deep probabilistic analysis of single-cell data, scirpy for T-cell receptor analysis, and squidpy for spatial omics analysis. We are looking forward to expanding with more major libraries and frameworks which fit our vision soon.

What are we doing?

Our first priority is to build a strong and lasting community around the core tools powering single cell data analysis today. -The knowledge to build and maintain these tools should be shared among many to avoid single points of failures. -Therefore, we are creating open community channels, creating shared infrastructure to ease package development, and building tooling to make creation of scverse based packages easier. -Furthermore, to bring the community together we are planning workshops and hackathons which will be open to the general community. -As we grow, we are hoping to recruit more members into governance roles as well as find even more ways to support and connect our community of developers and users.

There are already a few visible outcomes of our joint work including improved -mudata performance and -mudata documentation. Additionally, -scvi-tools is now using MuData for the representation of multimodal data. -Scanpy has gained new workshop notebooks, and, moreover, we have started -a collection of learning resources for scverse libraries. -We’ve also prepared -a template for developers -to help them to jump-start their new libraries.

Who is a part of scverse?

scverse is explicitly an effort beyond just a single research group. -As a community effort we strive for interoperability, shared growth, and democratized governance. -In our initial form, we have divided responsibilities into several roles, including:

Isaac Virshup, Danila Bredikhin and Lukas Heumos form the steering committee and also belong to the core developers together with Adam Gayoso, Giovanni Palla, Gregor Sturm, and Ilia Kats. The core developers have made significant contributions to the ecosystem and are jointly developing and maintaining the major libraries.

Our management committee, consisting of Fabian Theis, Oliver Stegle, Nir Yosef, Alex Wolf and Francesca Finotello, are providing resources and academic freedom to scverse to develop our tools.

Aviv Regev, Sarah Teichmann, Dana Pe’er and Bonnie Berger are our scientific advisory board which helps shaping the overall vision and defining the right priorities.

How can I join and contribute?

We’re particularly excited about the community coming together for this effort with so many brilliant people involved who design tools, write code, manage and analyse data and visualise results. Please ask usage questions on our Discourse forum, developer questions on our Zulip chat and make sure to follow us on Twitter to keep track of scverse updates.

scverse is very much open to contributions in all areas by everyone. -We strongly believe in diversity of all kinds being a requirement and a strong benefit for a healthy community. Hence, we embrace people from all backgrounds and experiences, who challenge each other’s assumptions with fresh perspectives. We’re committed to fair treatment and access for all members of the scverse community which is reflected in our code of conduct. A sense of belonging is important to us, so we strive to actively foster a community where everyone is and feels welcomed, respected, supported, and valued. We want to especially encourage people from underrepresented backgrounds to contribute and to reach out.

\ No newline at end of file diff --git a/blog/index.html b/blog/index.html deleted file mode 100644 index ec0aff1..0000000 --- a/blog/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Blogs - - -

Blog

May 17, 2022

Hello world

Introducing scverse
\ No newline at end of file diff --git a/events/2022_05_hackathon/index.html b/events/2022_05_hackathon/index.html deleted file mode 100644 index 0eb3bf2..0000000 --- a/events/2022_05_hackathon/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Scverse Hackathon 2022-05 Munich - -

Scverse Hackathon 2022-05 Munich

May 02, 2022

Welcome

Join us for the scverse Hackathon taking place from Monday, May 2nd, 9:00 AM to Tuesday, May 3rd, afternoon In Munich. -The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Hackathon checklist

  • Check that you agree with the scverse code of conduct.
  • Ensure that you have a Github account.
  • Join our zulip where you’ll be added to the hackathon stream. Say hi if this is your first time on the scverse zulip!
  • Have python and any scverse package that you might work on installed.
\ No newline at end of file diff --git a/events/2022_12_hackathon/index.html b/events/2022_12_hackathon/index.html deleted file mode 100644 index e6e877e..0000000 --- a/events/2022_12_hackathon/index.html +++ /dev/null @@ -1,6 +0,0 @@ -Scverse Hackathon 2022-12 Innsbruck - -

Scverse Hackathon 2022-12 Innsbruck

December 08, 2022

Welcome

Join us for the scverse Hackathon taking place from Thursday, December 8th, 10:00 AM to Friday, December 9th, afternoon In Innsbruck. -The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Hackathon checklist

  • Check that you agree with the scverse code of conduct.
  • Ensure that you have a Github account.
  • Join our zulip where you’ll be added to the hackathon stream. Say hi if this is your first time on the scverse zulip!
  • Have python and any scverse package that you might work on installed.
\ No newline at end of file diff --git a/events/2023_04_hackathon/index.html b/events/2023_04_hackathon/index.html deleted file mode 100644 index e59fc8a..0000000 --- a/events/2023_04_hackathon/index.html +++ /dev/null @@ -1,5 +0,0 @@ -Scverse Hackathon 2023-04 Heidelberg - -

Scverse Hackathon 2023-04 Heidelberg

April 26, 2023

Welcome

Join us for the scverse Hackathon taking place from Wednesday, April 26th, 12:00 PM to Friday, April 28th, afternoon at BioQuant (Neuenheimer Feld 267, 69120 Heidelberg, Germany).

The scverse hackathon is free. The event was invite only. We will try to make future editions open to everyone.

Event Schedule

  • Wednesday, April 26th (SR041)

    • 13:30 – 14:00 — PI introductions (Julio Saez-Rodriguez, Wolfgang Huber)
    • 14:00 – 14:30 — Hackathon introduction
    • 14:30 – 15:00 — State of the scverse + Q&A
    • 15:00 – 15:30 — Coffee break
    • 15:30 – 18:30 — Split into groups and hack
    • 18:30 – 19:00 — Short updates from teams

  • Thursday, April 27th (SR042 & SR044)

    • 08:30 – 09:00 — Coffee in the morning
    • 09:00 – 12:00 — Hack
    • 12:00 – 13:00 — Lunch + group photo
    • 13:00 – 15:30 — Hack + short updates
    • 15:30 – 16:00 — Coffee break
    • 16:00 – 18:30 — Hack + short updates
    • 19:30 — Group dinner

  • Friday, April 28th (SR042 & SR043)

    • 08:30 – 09:00 — Coffee in the morning
    • 09:00 – 12:00 — Hack
    • 12:00 – 13:00 — Lunch
    • 13:00 – 15:00 — Hack
    • 15:30 – 16:00 — Updates from teams
    • 16:00 — Coffee / departure
    • 16:30 — Feedback and brainstorming session
    • 19:00 — Self-organized going out

Hackathon Focus Areas

  1. Interoperability - Improve compatibility with other languages and tools.
  2. Biological Knowledge Representation - Enhance the integration of biological information in the scverse ecosystem.
  3. House keeping - Solve the issues that were forgotten about

Interoperability Tasks

  • Develop AnnData/MuData reader for Julia.
  • Develop AnnData/MuData reader for Bioconductor/R.
  • Create OME-ZARR reader and writer in R using Rarr.
  • Establish a test suite of scverse data files for various implementations.

Knowledge Representation Tasks

  • Develop a backend for BioCypher output and frontend Python package for annotating AnnData.
  • Enable access to genomic annotations through Bioconductor AnnotationHub.
  • Implement knowledge-guided sparsity for factor models.

House keeping Tasks

  • Integrating scverse tutorials
  • Implement scverse example datasets package
  • Improve cookiecutter template
  • Generate scverse branding content
  • Add events page to scverse website

See this hackmd for more information.

Hackathon checklist

  • Check that you agree with the scverse code of conduct.
  • Ensure that you have a Github account.
  • Join our zulip where you’ll be added to the hackathon stream. Say hi if this is your first time on the scverse zulip!
  • Have python and any scverse package that you might work on installed.
\ No newline at end of file diff --git a/events/index.html b/events/index.html deleted file mode 100644 index 07f6bc5..0000000 --- a/events/index.html +++ /dev/null @@ -1,11 +0,0 @@ -Events - - -

Events

Open community meeting

Scverse community meetings happen every second Tuesday at 6pm CET and are open to -everyone! If you are new to scverse, these meetings are a great way to get to know -the people behind the project.

We usually start off the meetings with a short presentation about a development-related -topic or a new ecosystem package.

The meetings have an open agenda. If -you would like to bring up a topic, feel free to add it before or during the meeting!

Agenda, next dates, meeting notes and zoom link are available from the -meeting document.

Upcoming and past events

April 26, 2023

Scverse Hackathon 2023-04 Heidelberg

Hackathon on interoperability and knowledge representation
December 08, 2022

Scverse Hackathon 2022-12 Innsbruck

Hackathon on documentation
May 02, 2022

Scverse Hackathon 2022-05 Munich

Hackathon on scverse cookiecutter template
\ No newline at end of file diff --git a/index.html b/index.html deleted file mode 100644 index 8c73615..0000000 --- a/index.html +++ /dev/null @@ -1,9 +0,0 @@ -scverse - -
scverse -Foundational tools for single-cell omics data analysis
Core packages
anndata

Standard for annotated matrices

mudata

Multimodal data format

scanpy

Single-cell analysis framework

muon

Multi-omics analysis framework

scvi-tools

Single-cell machine learning framework

scirpy

Single-cell immune sequencing analysis framework

squidpy

Spatial single cell analysis

View all scverse packages
Ecosystem

A broader ecosystem of packages builds on the scverse core packages. These tools implement models and analytical approaches to tackle challenges in spatial omics, regulatory genomics, trajectory inference, visualization, and more.

Continue to scverse ecosystem
Mission

scverse is a consortium of foundational tools (mostly in Python) for omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.

Read more about scverse
Team

scverse is a community project currently governed by the developers of the core packages. Please reach out if you’d like to be involved!

Learn more about scverse community
References

scverse tools are used in numerous research and industry projects across the globe and are referenced in thousands of academic publications. Consider consulting the following references for more information about core scverse libraries and citing the relevant articles when using them in your work:

\ No newline at end of file diff --git a/join/index.html b/join/index.html deleted file mode 100644 index d9f1311..0000000 --- a/join/index.html +++ /dev/null @@ -1,4 +0,0 @@ -Join scverse - -

Join scverse

 GitHub

Follow our organisation on GitHub

 Twitter

Follow us on Twitter

 Zulip

Chat with us on Zulip

 Discourse

Ask questions on Discourse

 YouTube

Subscribe to our YouTube channel

You can also reach the steering council at: steering-council@scverse.org

\ No newline at end of file diff --git a/learn/index.html b/learn/index.html deleted file mode 100644 index 0f86565..0000000 --- a/learn/index.html +++ /dev/null @@ -1,37 +0,0 @@ -Getting Started - -

Getting Started

If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core pacakges. -For more tutorials as well as API documentation and user guides, see the sites of individual packages.

You can also find recordings of past talks and workshops on our YouTube channel.

Tutorials

Data structures

These tutorials teach you how to work with scverse data structures. -If you are new to Python and/or scverse, we recommend you read the -"getting started" and "axes" tutorials first.

Axes in AnnData and MuData

In this tutorial we showcase operations on independent AnnData objects -(scRNAseq matrix + metadata), demonstrating how various processing -workflows can be stored in one MuData object.

Working with scverse objects in backed mode

In this tutorial, we demonstrate working with scverse data objects -without loading full datasets. (AnnData and MuData are saved as .h5ad and .h5mu files)

Getting started with AnnData

This tutorial helps you to explore the structure and content of single-cell -data analysis results in a *.h5ad file using AnnData, Scanpy, and Python.

Concatenation

In this notebook we showcase how to perform concatenation, meaning to -keep all sub elements of each object, and stack these elements in an -ordered way.

Concatenation of multimodal data

This tutorial shows how you can concatenate 2 MuData objects that may represent complementary -slices of the same dataset or 2 modalities into one AnnData.

scRNA-seq

The following tutorials show show to analyze single-cell gene expression data.

Compositional analysis

This tutorial introduces compositional analysis at cell identity -cluster level, based on known cell types or states affected by -perturbations.

Batch-effect removal with scvi-tools

In this tutorial, we demonstrate how to use scvi-tools to fit a model to single-cell count data, -correct batch effects, and perform differential gene expression analysis.

Pseudo-bulk differential expression and functional analysis

This notebook showcases decoupler for pathway and TF enrichment on ~5k -Blood myeloid cells from healthy and COVID-19 infected patients.

Pseudotemporal ordering

This tutorial show how a pseudotime can be constructed and compares different pseudotimes.

Perturbation modeling

This tutorial covers 3 approaches using single-cell perturbation data: -Augur (identify affected cell types), scGen (predict transcriptional response), -Mixscape (quantify CRISPR sensitivity).

Preprocessing, clustering and cell-type annotation

This fundamental tutorial covers common analysis steps: quality control, -normalization, feature selection, dimensionality reduction, clustering, -and cell-type annotation.

RNA velocity

This tutorial guides you through how RNA velocity can be inferred from single cell RNA-seq data -using scVelo.

Spatial

Analyze spatial data generated with different technologies

Spatial analysis with squidpy

This tutorial demonstrate how to use squidpy to analyse transcriptomics -data with spatial resolution.

Spatial analysis at subcellular resolution

This tutorial shows how to use bentotools to study -gene expression at subcellular resolution.

Adaptive immune cell receptor

Tutorials for analyzing single-cell B-cell and T-cell receptor sequencing data

Single-cell T-cell receptor analysis with scirpy

In this tutorial, we show how to perfrom QC on scTCR-seq data, -define clonotype, cluster receptors by their sequence similarity -and compute repertoire overlaps between patients.

Surface proteins

CITE-seq analyses

CITE-seq integration

These notebooks showcase CITE-seq analysis of PBMCs with dsb -normalization, MOFA+ data integration, and weighted nearest neighbors -handling multimodal embeddings.

ATAC-seq

Analyse chromatin accessibility data

Joint analysis of paired and unpaired multiomic data with MultiVI

This tutorial shows how to read multiomic data, create a joint object with -paired/unpaired data, train MultiVI model, visualize latent space, -and run differential analyses.

Processing chromatin accessibility

This chapter shows multimodal single-cell gene expression and -chromatin accessibility analysis. In this notebook, scATAC-seq -data processing is described.

Tips & Tricks

Useful tips for data analysis with scverse tools that are independent of specific packages.

Advanced plotting

This tutorial explains how to customize matplotlib plots generated -by scanpy or other scverse libraries.

Plotting in scanpy

This tutorial explores the visualization possibilities of scanpy, including -embeddings and the visualization of marker genes and differentially expressed genes.

Interoperability

This document lists resources for conversion to other data formats and programming -languages, e.g. R, Julia, ...

\ No newline at end of file diff --git a/main.min.css b/main.min.css deleted file mode 100644 index 0ddc88d..0000000 --- a/main.min.css +++ /dev/null @@ -1 +0,0 @@ -@font-face{font-family:inter;src:url(fonts/Inter/Inter-VariableFont_slnt,wght.ttf)}.dropdown-menu{margin-top:.3rem!important;padding:1rem .5rem;background-color:#f0f0f0;box-shadow:0 8px 16px rgba(0,0,0,5%);border:0;border-radius:.5rem;transition:all 200ms ease-in-out!important}.dropdown-menu a{color:#555;border-radius:.5rem}.dropdown-menu a:hover{background-color:#f0f0f0;color:#000}.dropdown-menu a:hover{background-color:#e0e0e0;color:#000}.i-zulip::before{background:url(/img/icons/zulip.svg)no-repeat;transition:background 200ms ease-out;display:inline-block;height:1rem;width:1rem;content:"";padding:0;margin:0}.i-discourse::before{background:url(/img/icons/discourse.svg)no-repeat;transition:background 200ms ease-out;display:inline-block;height:1rem;width:1rem;content:"";padding:0;margin:0}.card:hover .i-zulip::before{background:url(/img/icons/zulip_inv.svg)no-repeat}.card:hover .i-discourse::before{background:url(/img/icons/discourse_inv.svg)no-repeat}.btn-github:hover{border-color:#171b21;background-color:#171b21}.btn-discourse:hover{background-color:#f7f0b1;color:#000}.btn-zulip:hover{border-color:#62a3f0;background-color:#62a3f0}.btn-twitter:hover{border-color:#469be5;background-color:#469be5}.btn-youtube:hover{border-color:#e03021;background-color:#e03021}p{font-family:inter,Open Sans,sans-serif}h1{font-weight:800}.section-paragraph{font-size:1.1rem;margin-bottom:1rem}.section-paragraph strong{font-weight:475;font-size:1.2rem}a .more{display:inline-block;margin:0;font-size:.8rem;font-weight:800;font-family:inter,sans-serif;color:#555;transition:all 200ms ease-in-out;padding:.5rem;margin-left:-.5rem;border-radius:.5rem}a .more:after{content:"\232A";font-size:.6rem;transition:all 200ms ease-in-out;padding-left:.2rem}a .more:hover{color:#000;background-color:#f0f0f0}a .more:hover:after{padding-left:.4rem}@media(max-device-width:40rem){a .more{background-color:#f5f5f5}}.contributor-list>a{text-decoration:none}html,body{width:100%;height:100%;-webkit-font-smoothing:antialiased;scroll-behavior:smooth;-webkit-scroll-behavior:smooth;-moz-osx-font-smoothing:grayscale}.nav-buttons>li{padding:.5rem}.nav-buttons>li>a{font-family:inter,sans-serif;color:#555;padding:.5rem .8rem!important;border-radius:.5rem;transition:all 300ms ease-in-out,transform 100ms ease-in-out}.nav-buttons>li>a:hover,.nav-buttons>li>a:active{background-color:#f0f0f0;color:#000}.nav-buttons>li>a:active{transform:scale(.95)}.nav-buttons>li>a:hover{color:#000}.nav-buttons>li>a.active{transform:scale(.95);background-color:#e0e0e0;color:#000}#join-button{color:#fff;background-color:#4557c4;background:linear-gradient(135deg,#262fb5,#74c8fa);transition:background 200ms ease-out}#join-button:hover{background:linear-gradient(135deg,#74c8fa,#d4ac00);color:#fff}#scverse-logo{width:3rem;height:3rem;background:url(/img/icons/scverse_bw_logo.svg)no-repeat;transition:background 200ms ease-out}#scverse-logo:hover{background:url(/img/icons/scverse_color_logo.svg)no-repeat}.logo-name{color:#000;font-size:1.5rem;line-height:1.5rem;font-family:inter,sans-serif;font-weight:500;letter-spacing:.15rem;margin-left:1rem}.dropdown:hover .dropdown-menu{transition:background 200ms ease-out;display:block;margin-top:0}body{margin:0;display:flex;flex-direction:column}body #wrapper{width:100%;flex:1}body #wrapper #content{display:flex;flex-direction:column;justify-content:center;align-items:center;align-self:center}body #wrapper #content #cover{max-width:1400px;width:92%}@media(max-device-width:40rem){body #wrapper #content #cover{max-width:1400px;width:92%}}body #wrapper #content #cover #cover-heading{margin-top:10%;max-width:1400px;border-radius:1rem;background:linear-gradient(90deg,#f0f0f0,#f0f0f0);padding:6rem 4rem}@media(max-device-width:40rem){body #wrapper #content #cover #cover-heading{margin-top:10%}}@media(max-device-width:40rem){body #wrapper #content #cover #cover-heading{padding:2rem 1rem}}body #wrapper #content #cover #cover-heading #title #title-text #title-name{font-size:6rem;font-family:inter,sans-serif;font-weight:900;letter-spacing:.2rem}@media(max-device-width:40rem){body #wrapper #content #cover #cover-heading #title #title-text #title-name{letter-spacing:.1rem;font-size:2rem}}body #wrapper #content #cover #cover-heading #title #title-text #title-desc{display:block;font-family:inter,sans-serif;font-size:1.4rem;color:#333}@media(max-device-width:40rem){body #wrapper #content #cover #cover-heading #title #title-text #title-desc{font-size:.8rem}}body #wrapper #content #cover #cover-heading #badges{display:flex;flex-wrap:wrap;gap:1rem;margin:4rem 0}@media(max-device-width:40rem){body #wrapper #content #cover #cover-heading #badges{margin:1rem 0;padding:0;width:100%}}body #wrapper #content #cover section{max-width:800px;width:80%;margin:0 auto;margin-top:5%}@media(max-device-width:40rem){body #wrapper #content #cover section{margin-top:15%}}body #wrapper #content #cover section .section-heading{font-size:1.3rem;text-transform:uppercase;color:#333;font-weight:700;font-family:inter,sans-serif;transition:all 200ms ease-in-out}body #wrapper #content #cover section .section-heading.clickable-heading:hover{color:#555;cursor:pointer}body #wrapper #content #cover section .section-content{margin-top:1rem}body #wrapper #content #cover section .section-content .tiles-list{display:grid}body #wrapper #content #cover section .section-content .tiles-list a{text-decoration:none}body #wrapper #content #cover #packages{margin-top:15%}body #wrapper #content #cover #packages #packages-list .card{display:flex;flex-direction:row;align-items:center;background-color:#f0f0f0;border-radius:.5rem;transition:all 200ms ease-in-out}@media(max-device-width:40rem){body #wrapper #content #cover #packages #packages-list .card{min-height:6rem}}body #wrapper #content #cover #packages #packages-list .card .package-icon{transition:all 200ms ease-in-out;align-items:center;justify-content:center;padding:auto;display:flex;min-width:6rem;max-width:6rem}@media(max-device-width:40rem){body #wrapper #content #cover #packages #packages-list .card .package-icon{display:none}}body #wrapper #content #cover #packages #packages-list .card .package-icon img{max-width:4rem;height:4rem}body #wrapper #content #cover #packages #packages-list .card .package-text .package-name{font-family:inter,sans-serif;color:#333}body #wrapper #content #cover #packages #packages-list .card .package-text .package-desc{font-family:inter,sans-serif;font-size:.9rem;color:#555}body #wrapper #content #cover #packages #packages-list .card:hover{cursor:pointer;background-color:#d9d9d9;transform:scale(1.05)}body #wrapper #content #cover #packages #packages-list .card:hover .package-icon{transform:scale(1.1)}body #wrapper #content #cover #packages #packages-list .card#anndata-tile:hover{background-color:rgba(229,134,75,.2)}body #wrapper #content #cover #packages #packages-list .card#scanpy-tile:hover{background-color:rgba(224,85,89,.2)}body #wrapper #content #cover #packages #packages-list .card#mudata-tile:hover{background-color:rgba(74,178,116,.2)}body #wrapper #content #cover #packages #packages-list .card#muon-tile:hover{background-color:rgba(108,241,161,.2)}body #wrapper #content #cover #mission .section-content p{font-size:1.1rem}body #wrapper #content #cover #team .section-content .section-paragraph #team-list{display:inline}body #wrapper #content #cover #team .section-content .section-paragraph a{border-bottom:1px solid #aaa;transition:border 200ms,color 200ms}body #wrapper #content #cover #team .section-content .section-paragraph a:hover,body #wrapper #content #cover #team .section-content .section-paragraph a:active{color:#000;border-bottom:1px solid #000}body #wrapper #content #cover #references #refs-list .ref-tile{display:flex;margin:0 -.8rem;padding:.8rem;width:100%;min-height:1rem;align-items:center;background-color:#0000;color:#333;transition:all 200ms ease-in-out;border-radius:.5rem;font-size:.9rem}body #wrapper #content #cover #references #refs-list .ref-tile:hover{cursor:pointer;background-color:#e0e0e0}body #wrapper span.backticked{font-family:Inter,sans-serif;color:#333;font-weight:500}body #wrapper p>a{text-decoration:none;color:inherit;border-bottom:1px solid #aaa;transition:border 200ms,color 200ms}body #wrapper p>a:hover,body #wrapper p>a:active{border-bottom:1px solid #000}body header{height:auto;width:100%;display:flex;flex-direction:column;justify-content:center;align-items:center;align-self:center}body header #banner{width:100%;display:flex;justify-content:center;align-items:center;background:linear-gradient(135deg,#262fb5,#74c8fa);color:rgba(255,255,255,.8);font-weight:600;font-family:inter,sans-serif;padding:1rem 0;box-shadow:inset 0 -.5rem 1rem .05rem rgba(0,0,0,.1);margin-bottom:1rem}body header #banner a{color:inherit;text-decoration:none;border-bottom:1px solid rgba(255,255,255,.8)}body header #banner a:hover,body header #banner a:active{color:#fff;border-bottom:1px solid #fff}body footer{height:auto;width:100%;margin-top:10rem;background-color:#f0f0f0;display:flex;flex-direction:column;justify-content:center;align-items:center;align-self:center}body footer #footer-content{width:80%;padding:2%}@media(max-device-width:40rem){body footer #footer-content{width:92%}}body footer #footer-content div{max-width:800px;margin:1rem auto;color:#333;text-align:left}body footer #footer-content div ul{list-style:none}body footer #footer-content div a,body footer #footer-content div p{margin:.2rem 0;font-family:inter,sans-serif;font-weight:500;font-size:.9rem}body footer #footer-content div a{color:inherit;text-decoration:none;transition:color 200ms}body footer #footer-content div h5{color:#777}body footer #footer-content div li{color:#aaa}body footer #footer-content div li a{color:#777}body footer #footer-content div li a:hover{color:#000}body footer #footer-content div.signature{margin-bottom:0;text-align:right}body footer #footer-content div.acknowledgement{margin-top:0}body footer #footer-content div.acknowledgement p{margin-top:0;color:#aaa}#join-content .card{transition:all 200ms ease-in-out;color:navtext}#join-content .card h5{font-family:inter,sans-serif;font-weight:700}#join-content .card:hover{background:#78cbd9!important;transform:scale(1.02)}#join-content .card#github:hover{color:#fff;background-color:#171b21!important}#join-content .card#twitter:hover{color:#fff;background-color:#469be5!important}#join-content .card#zulip:hover{color:#fff;background-color:#62a3f0!important}#join-content .card#discourse:hover{background-color:#f7f0b1!important}#join-content .card#youtube:hover{color:#fff;background-color:#e03021!important}#page-content{display:flex;flex-direction:column;max-width:800px;width:80%;margin-top:3rem;font-family:inter,sans-serif}@media(max-device-width:40rem){#page-content{max-width:1400px;width:92%;gap:1rem}}#page-content.items-list a{text-decoration:none}#page-content.items-list a:first-of-type{margin-top:3rem}#page-content .page-item{display:flex;flex-direction:row;font-family:inter,sans-serif;margin:0 -1rem;padding:1rem;background-color:#0000;transition:all 200ms ease-in-out;border-radius:.5rem}@media(max-device-width:40rem){#page-content .page-item{flex-direction:column;align-items:flex-start;justify-content:center;margin:0 -.5rem;padding:.5rem;padding-bottom:1.3rem}#page-content .page-item h2{margin:.5rem 0!important}}#page-content .page-item:hover{cursor:pointer;background-color:#e0e0e0}@media(max-device-width:40rem){#page-content .page-item{background-color:#f5f5f5}}#page-content .page-item h2{color:#333;margin:0 0 .5rem;line-height:1.5rem}#page-content .page-item span{font-size:1rem;color:#777;line-height:1.5rem}#page-content .page-item .page-item-date{flex:1;line-height:1.5rem}#page-content .page-item .page-item-content{flex:2;display:flex;flex-direction:column;font-size:1rem}#page-content .page-item .page-item-content h2{font-size:1.6rem}#page-content .post .post-subtitle{display:flex;flex-direction:row;align-items:center;justify-content:flex-start;line-height:1.5rem;gap:.5rem;color:#777}#page-content .post .post-subtitle .rss-icon{width:1rem;height:auto}#page-content .post .post-subtitle .rss-icon a{width:100%;display:flex;align-items:center;text-decoration:none}#page-content .post .post-subtitle .rss-icon a svg{fill:#777}#page-content .post .post-subtitle .rss-icon a:hover svg{fill:#000}#page-content .post .post-content{margin:3rem 0;font-size:1.1rem}#page-content .post .post-content span.backticked{font-size:1.2rem;line-height:1.1rem}#page-content .post .post-content p,#page-content .post .post-content div,#page-content .post .post-content ul,#page-content .post .post-content ol{font-family:inter,Open Sans,sans-serif}@media(max-device-width:40rem){#page-content .post .post-content{font-size:1rem;line-height:1.8rem}}#page-content .post h2,#page-content .post h3,#page-content .post h4{font-family:inter,sans-serif;margin:4rem 0 1rem}#page-content .post a{font-family:inter,sans-serif;color:#333}#page-content .post a:hover{color:#000}#packages-content #packages-list{display:flex;flex-direction:column;gap:5rem}#packages-content #packages-list .package-section{display:flex;flex-direction:row;margin:.5rem 0;gap:3rem}#packages-content #packages-list .package-section:first-of-type{margin-top:2rem}#packages-content #packages-list .package-section .package-img{flex:1;transition:all 200ms ease-in-out}#packages-content #packages-list .package-section .package-img img{display:block;padding:.5rem;flex:none;align-self:center;object-fit:contain;margin:auto;max-width:100%;max-height:225px}@media(max-device-width:40rem){#packages-content #packages-list .package-section .package-img{display:none}}#packages-content #packages-list .package-section .package-info{flex:3;display:flex;flex-direction:column;align-items:flex-start;gap:0}#packages-content #packages-list .package-section .package-info .package-tile{border-radius:1rem}#packages-content #packages-list .package-section .package-info .package-tile .package-text .package-name{font-family:inter,sans-serif;font-size:2rem;font-weight:800;color:#000;display:block}#packages-content #packages-list .package-section .package-info .package-tile .package-text .package-details{display:block;font-size:1.1rem;margin:1rem 0;color:#333}@media(max-device-width:40rem){#packages-content #packages-list .package-section .package-info .package-tile .package-text .package-details{font-size:1rem;line-height:1.8rem}}#packages-content .package-links a{display:inline-block;background-color:#f0f0f0;text-decoration:none;font-size:1rem;color:#333;padding:.4rem .8rem;margin:.5rem 0;text-align:center;border-radius:.5rem;transition:all 200ms ease-in-out}#packages-content .package-links a:hover,#packages-content .package-links a:active{color:#000;background-color:#d9d9d9}#eco-table tbody{border-top:0}#tutorials-content h1,#tutorials-content h2{margin-bottom:1rem!important}#tutorials-content #ecosystem-tutorials input{height:3.2rem;outline:none;border-color:#f0f0f0;-webkit-box-shadow:none;box-shadow:none}#tutorials-content #ecosystem-tutorials input:focus{border-color:silver}#tutorials-content .tutorials-list{display:grid;flex-wrap:wrap;margin-bottom:5rem;grid-auto-flow:row;grid-template-columns:1fr 1fr 1fr;gap:1rem}@media(max-width:50rem),(max-device-width:40rem){#tutorials-content .tutorials-list{grid-template-columns:1fr}}#tutorials-content .tutorials-list .tutorial-item{border-radius:1rem;background-color:#fbfbfb;transition:all 200ms ease-in-out;justify-content:flex-start;height:25rem}#tutorials-content .tutorials-list .tutorial-item a{color:#555;text-decoration:none;height:100%}#tutorials-content .tutorials-list .tutorial-item img{width:90%;height:40%;object-fit:contain;margin:1.5rem 1rem .2rem}#tutorials-content .tutorials-list .tutorial-item:hover,#tutorials-content .tutorials-list .tutorial-item:active{background-color:#f0f0f0;transform:scale(1.02)}#tutorials-content .tutorials-list .tutorial-item:hover h5,#tutorials-content .tutorials-list .tutorial-item:active h5{color:#000}#tutorials-content .tutorials-list .tutorial-item:hover p,#tutorials-content .tutorials-list .tutorial-item:active p{color:#000}#tutorials-content .tutorials-list .tutorial-item .card-body{height:60%;flex:1;overflow:hidden}#tutorials-content .tutorials-list .tutorial-item .card-body h5{font-size:1.1rem;font-weight:900;transition:all 200ms ease-in-out}#tutorials-content .tutorials-list .tutorial-item .card-body p{flex:1;width:100%;overflow:hidden;display:-webkit-box;-webkit-line-clamp:6;-webkit-box-orient:vertical;font-size:.8rem;transition:all 200ms ease-in-out}#tutorials-content .tutorials-list .tutorial-item .card-body>p{font-size:.8rem}#people-content .team .team-text{margin:1rem 0}#people-content .team .team-list{font-size:1.1rem;display:flex;justify-content:center;flex-wrap:wrap;gap:.5rem;justify-content:flex-start}#people-content .team .team-list .person-chip{background-color:#f0f0f0;text-decoration:none;color:#333;padding:.4rem;text-align:center;border-radius:.5rem;transition:all 200ms ease-in-out;font-size:1rem;font-family:inter,sans-serif}#people-content .team .team-list .person-chip:hover{color:#000;background-color:#d9d9d9}#people-content .team .team-list a{text-decoration:none} \ No newline at end of file diff --git a/packages/index.html b/packages/index.html deleted file mode 100644 index 04c2364..0000000 --- a/packages/index.html +++ /dev/null @@ -1,70 +0,0 @@ -Packages - -

Packages

Data structures

Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability.
anndata -AnnData is a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.
GitHub -Documentation -PyPI -Conda
mudata -MuData is a format for annotated multimodal datasets where each modality is represented by an AnnData object. MuData’s reference implementation is in Python, and the cross-language functionality is achieved via HDF5-based .h5mu files with libraries in R and Julia.
GitHub -Documentation -PyPI -Conda -Muon.jl
spatialdata -SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This repository contains the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.
GitHub -Documentation -PyPI -spatialdata-io

Modality-specific extensions

In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for Adaptive Immune Receptor Repertoire (AIRR) data. Representations for other data types (e.g. scATAC-seq) will follow.

Packages maintained by core team

These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability.
scanpy -Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
GitHub -Documentation and tutorials -PyPI -Conda
muon -muon is a Python framework for multimodal omics analysis. While there are many features that muon brings to the table, there are three key areas that its functionality is focused on.
GitHub -Documentation -Tutorials -PyPI -Website
scvi-tools -scvi-tools is a library for developing and deploying machine learning models based on PyTorch and AnnData. With an emphasis on probablistic models, scvi-tools steamlines the development process via training, data management, and user interface abstractions. scvi-tools also contains easy-to-use implementations of more than 14 state-of-the-art probabilistic models in the field.
GitHub -Documentation and tutorials -PyPI -Website
scirpy -Scirpy is a scalable toolkit to analyse T-cell receptor or B-cell receptor repertoires from single-cell RNA sequencing data. It seamlessly integrates with scanpy and provides various modules for data import, analysis and visualization.
GitHub -Documentation and tutorials -PyPI -Conda
squidpy -Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.
GitHub -Documentation and tutorials -PyPI

Ecosystem packages maintained by scverse community

Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).

This listing is a work in progress. See scverse/ecosystem-packages for inclusion criteria, and to submit more packages.

PackageDescription
CellOracleA computational tool that integrates single-cell transcriptome and epigenome profiles -to infer gene regulatory networks (GRNs), critical regulators of cell identity.
CellRankCellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. -It contains two main modules - kernels compute cell-cell transition probabilities and estimators generate -hypothesis based on these.
Cell_BLASTCell BLAST is a cell querying tool for single-cell transcriptomics data.
CirrocumulusCirrocumulus is an interactive visualization tool for large-scale single-cell genomics data.
DoubletDetectionDoubletDetection is a Python3 package to detect doublets (technical errors) in single-cell -RNA-seq count matrices.
MowgliPaired single-cell multi-omics data integration with Optimal Transport-flavored Nonnegative Matrix Factorization
MultiveloA mechanistic model of gene expression that extends the popular RNA velocity -framework by incorporating epigenomic data.
PathMLAn open-source toolkit for computational pathology and machine learning.
PyDESeq2PyDESeq2 is a python package for bulk RNA-seq differential expression analysis. It is a re-implementation -from scratch of the main features of the R package DESeq2 (Love et al. 2014).
SC2SpaSC2Spa is a deep learning-based tool for predicting the spatial coordinates of single cells based on transcriptome. -Two paired single cell and spatial transcriptomic datasets are required to run SC2Spa. SC2Spa is trained on a ST reference -dataset to learn the relationship of gene expression and spatial coordinates. The trained fully-connected neural network -can be used to predict the locations of a single cell with only the transcriptomic profile as input. The predicted locations -of single cells can be further used to study the communication of the single cells.
SnapATAC2

SnapATAC2 is the successor of the SnapATAC R package, featuring:

  • Faster and less memory usage, scale to >1M cells.
  • Improved dimension reduction and sampling algorithm.
anndata for RA ‘reticulate’ wrapper for the Python package ‘anndata’. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format.
bento-toolsA Python toolkit for subcellular analysis of spatial transcriptomics data
biolordbiolord (biological representation disentanglement) is a deep generative framework for disentangling known and unknown attributes in single-cell data.
cell2locationCell2location is a Bayesian model that can resolve fine-grained cell types in spatial transcriptomic data -and create comprehensive cellular maps of diverse tissues. Cell2location accounts for technical sources -of variation and borrows statistical strength across locations, thereby enabling the integration of single-cell -and spatial transcriptomics with higher sensitivity and resolution than existing tools.
cellxgeneCZ CELLxGENE Annotate (pronounced “cell-by-gene”) is an interactive data explorer for single-cell datasets, -such as those coming from the Human Cell Atlas.
dandeliondandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5’ data. -It streamlines the pre-processing, leveraging some tools from immcantation suite, and -integrates with scanpy/anndata for single-cell BCR/TCR analysis. It also includes a -couple of functions for visualization.
decouplerPython package to infer biological activities from omics data using a collection of methods.
dynamo-releaseInclusive model of expression dynamics with metabolic labeling based scRNA-seq / multiomics, -vector field reconstruction, potential landscape mapping, differential geometry analyses, -and most probably paths / in silico perturbation predictions.
epiScanpyEpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell -DNA methylation (for example scBS-seq) data.
hotspotHotspot is a tool for identifying informative genes (and gene modules) in a single-cell dataset.
infercnvpyInfer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
maxspinAn information theoretic approach to detecting spatially varying genes
moscotmoscot is a scalable toolbox for multiomics single-cell optimal transport applications.
omicverseOmicVerse is the fundamental package for multi omics included bulk and single cell analysis with Python. -The original name of the omicverse was Pyomic, but we wanted to address a whole universe of transcriptomics, -so we changed the name to OmicVerse, it aimed to solve all task in RNA-seq.
pegasusPegasus is a tool for analyzing transcriptomes of millions of single cells.
pySCENICpySCENIC is a lightning-fast python implementation of the SCENIC pipeline -(Single-Cell rEgulatory Network Inference and Clustering) which enables -biologists to infer transcription factors, gene regulatory networks and -cell types from single-cell RNA-seq data.
pychromVARA python pacakge for chromVAR.
rapids-singlecellA GPU acclerated python package for singlecell data analysis
scFatesA scalable python package for tree inference and advanced pseudotime analysis from scRNAseq data.
scGenscGen is a generative model to predict single-cell perturbation response -across cell types, studies and species.
scibEvaluating single-cell data integration methods
scTriangulatePython package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
scVeloscVelo is a scalable toolkit for RNA velocity analysis in single cells, based on Bergen et al., Nature Biotech, 2020.
scyanBiology-driven deep generative model for cell-type annotation in cytometry. -Scyan is an interpretable model that also corrects batch-effect and -can be used for debarcoding or population discovery.
sfairasfaira is a model and a data repository in a single python package.
sift-scSiFT is a computational framework which aims to uncover the underlying structure by filtering out previously exposed biological signals. -SiFT can be applied to a wide range of tasks, from (i) the removal of unwanted variation as a pre-processing step, through (ii) revealing hidden biological structure by utilizing prior knowledge with respect to existing signal, to (iii) uncovering trajectories of interest using reference data to remove unwanted variation.
Sobolev AlignmentSobolev alignment of deep probabilistic models for comparing single cell profiles from pre-clinical models and patients
spatial-eggplantPython package designed to transfer information from multiple spatial-transcriptomics data sets to a single reference representing a Common Coordinate Framework (CCF).
SymphonypySymphonypy is a pure Python port of Symphony label transfer algorithm for reference-based cell type -annotation.
tangramSpatial alignment and gene expression mapping of single cell transcriptomic data.
vitessceVitessce consists of reusable interactive views including a scatterplot, -spatial+imaging plot, genome browser tracks, statistical plots, and control -views, built on web technologies such as WebGL.
\ No newline at end of file diff --git a/people/index.html b/people/index.html deleted file mode 100644 index ac9610a..0000000 --- a/people/index.html +++ /dev/null @@ -1,46 +0,0 @@ -People - -

People

For people participating in and interacting with the consortium, there are different roles — from core developers to contributors and community members.

Core Team

The Core Team is governing scverse and is deeply involved in developing and maintaining scverse packages.

Philipp Angerer
Danila Bredikhin
Lukas Heumos
Ilia Kats
Martin Kim
Mikaela Koutrouli
Luca Marconato
Giovanni Palla
Anna Schaar
Gregor Sturm
Isaac Virshup

Steering Council

The Steering Council (SC) consists of a fixed number of core team members who have additional responsibilities to ensure the smooth running of the project.

Danila Bredikhin
Lukas Heumos
Isaac Virshup

Management Committee

Management Committee is committed to supporting scverse and is directly involved in investing in its progress.

Francesca Finotello
Oliver Stegle
Fabian Theis
Alex Wolf
Nir Yosef

Advisory Committee

Advisory Committee helps to shape the overall vision for scverse and to define its priorities.

Bonnie Berger
Dana Pe'er
Aviv Regev
Sarah Teichmann

Community

Everyone who uses scverse software is part of the community! There are multiple ways to engage with its other members. For a start, join us on our Discourse forum and keep an eye on our Twitter account for the events we organise.

Honorary Members

Former core team members who made essential contributions to scverse.

Adam Gayoso

Contributors

All this work makes sense only in the context of the larger community of contributors and users of scverse projects. Open-source scverse projects are open to contributions, and over 150 people have contributed to scverse packages.

Adam Gayoso -Alex Wolf -Alma Andersson -Anna Schaar -@brianhie -Can Ergen -Carlos Talavera-López -Danila -David S. Fischer -Davide Cittaro -Giovanni Palla -Gregor Sturm -Gökçen Eraslan -@ilia-kats -Isaac Virshup -Jan Lause -Jeffrey Regier -Jonathan Manning -Justin Hong -Karin Hrovatin -Kathy Wu -Kevin Yamauchi -@LucaMarconato -Lukas Heumos -@M0hammadL -MalteDLuecken -Maren Büttner -Marius Lange -Max Frank -@michalk8 -Philipp A. -Philipp Weiler -Pierre Boyeau -Romain Lopez -Sergei Rybakov -@talashuach -Tommaso Biancalani -Valeh Valiollah Pour Amiri -Valentine Svensson -Vitalii Kleshchevnikov -@zoepiran -Zoë Steier
\ No newline at end of file