Dana Pe'er Lab

All

67 repositories

Palantir
Public
Single cell trajectory detection
markov-chain dimensionality-reduction scrna-seq trajectory-generation diffusion-maps differentiation manifold-learning single-cell-genomics cell-fate-transitions scrna-seq-analysis
Jupyter Notebook
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GNU General Public License v2.0
•52•226•6•0•Updated Nov 26, 2024Nov 26, 2024
progressive-plasticity-crc-metastasis
Public
Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"
Jupyter Notebook
•1•8•2•0•Updated Nov 18, 2024Nov 18, 2024
WassersteinWormhole
Public
Transformer Based Embeddings of Wasserstein Distance
Python
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MIT License
•1•13•1•1•Updated Nov 4, 2024Nov 4, 2024
Brain-metastasis-TME
Public
Jupyter Notebook
•0•1•0•0•Updated Oct 30, 2024Oct 30, 2024
ENVI
Public
Python
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MIT License
•6•38•11•1•Updated Oct 16, 2024Oct 16, 2024
sharp
Public
A single-cell demultiplexing pipeline, the sharp (♯)
Jupyter Notebook
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MIT License
•1•0•1•1•Updated Sep 30, 2024Sep 30, 2024
segger_dev
Public
Python
•
MIT License
•0•0•0•0•Updated Sep 27, 2024Sep 27, 2024
spectra
Public
Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
Python
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MIT License
•17•158•18•5•Updated Jul 26, 2024Jul 26, 2024
Harmony
Public
Harmony framework for connecting scRNA-seq data from discrete time points
scrna-seq mnn batch-correction scrna-seq-analysis developmental-trajecotries
Jupyter Notebook
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GNU General Public License v2.0
•12•46•8•0•Updated Jul 13, 2024Jul 13, 2024
SEACells
Public
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
Jupyter Notebook
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GNU General Public License v2.0
•27•148•26•3•Updated Jun 28, 2024Jun 28, 2024
integrateCNV
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 27, 2024Jun 27, 2024
cellpose
Public
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•403•1•0•0•Updated May 13, 2024May 13, 2024
STAR
Public
RNA-seq aligner
C++
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MIT License
•506•1•0•0•Updated May 10, 2024May 10, 2024
benchkit
Public
Scripts for managing and processing large number of samples, also providing a CLI.
0•0•0•0•Updated May 9, 2024May 9, 2024
docker-cellranger
Public
Dockerized Cell Ranger
Shell
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MIT License
•3•0•0•0•Updated May 3, 2024May 3, 2024
ecosystem-packages
Public
Register pe'er lab packages to scverse ecosystem
Python
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BSD 3-Clause "New" or "Revised" License
•40•0•0•0•Updated Apr 15, 2024Apr 15, 2024
mssi
Public
Jupyter Notebook
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MIT License
•0•1•1•0•Updated Mar 19, 2024Mar 19, 2024
cytopus
Public
Single cell omics biology annotations
Jupyter Notebook
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MIT License
•2•2•0•0•Updated Jan 14, 2024Jan 14, 2024
PrismSpot
Public
Jupyter Notebook
•0•1•0•0•Updated Oct 24, 2023Oct 24, 2023
scKINETICS
Public
Code for scKINETICS (ISMB 2023)
expectation-maximization atac-seq single-cell-analysis gene-regulatory-network
Jupyter Notebook
•3•20•4•0•Updated Oct 23, 2023Oct 23, 2023
scing
Public
SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)
Python
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MIT License
•3•0•0•0•Updated Oct 5, 2023Oct 5, 2023
MERlin
Public
MERFISH decoding software
Python
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MIT License
•30•1•2•0•Updated Sep 19, 2023Sep 19, 2023
Treg_depletion_reproducibility
Public
Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023.
HTML
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MIT License
•0•2•0•0•Updated Jul 13, 2023Jul 13, 2023
SpectraReproducibility
Public
Notebooks for reproducing figures in the Spectra paper
Jupyter Notebook
•3•7•2•0•Updated Jun 7, 2023Jun 7, 2023
ArchR
Public
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
R
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MIT License
•140•4•0•0•Updated May 17, 2023May 17, 2023
pdac-progression
Public
Jupyter Notebook
•4•10•1•0•Updated Apr 28, 2023Apr 28, 2023
wdl-cellranger-arc
Public
WDLized Cell Ranger ARC
WDL
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MIT License
•1•0•0•0•Updated Apr 21, 2023Apr 21, 2023
wdl-cellranger-gex
Public
WDLized Cell Ranger GEX
WDL
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MIT License
•2•0•0•0•Updated Apr 11, 2023Apr 11, 2023
docker-cellranger-arc
Public
Dockerized Cell Ranger ARC
Shell
•1•0•0•0•Updated Apr 4, 2023Apr 4, 2023
Lineage_Plasticity_in_CRPC
Public
Jupyter Notebook
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GNU General Public License v3.0
•3•8•0•0•Updated Feb 15, 2023Feb 15, 2023