New domain page on Single-cell (#1413)

* Create single_cell.md * Update single_cell.md * Update single_cell.md * Update single_cell.md * Fix link for git. * Update single_cell.md Added section about formats * update the existing singl-cell doc * Update single_cell.md * Typo and clarity correction * author update * Update pages/your_domain/single_cell.md Co-authored-by: Bert Droesbeke <[email protected]> * Update pages/your_domain/single_cell.md Co-authored-by: Bert Droesbeke <[email protected]> * Update pages/your_domain/single_cell.md Co-authored-by: Bert Droesbeke <[email protected]> * Update pages/your_domain/single_cell.md Co-authored-by: Bert Droesbeke <[email protected]> * Author and affiliation corrected * Revert "Author and affiliation corrected" This reverts commit 8485a77. * author, affiliation and file named corrected * Titles capital removal * space in heading correction * Tools and resources correction * Update _data/tool_and_resource_list.yml Co-authored-by: Bert Droesbeke <[email protected]> * correction sceasy and registry NA block * added to sidebar * sceasy link correction * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * update tool list with cellranger and startsolo * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Update pages/your_domain/single_cell_sequencing.md Co-authored-by: Federico Bianchini <[email protected]> * Apply suggestions from code review Co-authored-by: Federico Bianchini <[email protected]> * Tool syntax correction * Update single_cell_sequencing.md * Update single_cell_sequencing.md * Update single_cell_sequencing.md * Update single_cell_sequencing.md * upade after Nazeeefa review * Update _data/tool_and_resource_list.yml Co-authored-by: Federico Bianchini <[email protected]> --------- Co-authored-by: Marc Broghammer <[email protected]> Co-authored-by: Vogel-lab <[email protected]> Co-authored-by: mtekman <[email protected]> Co-authored-by: Pavankumar Videm <[email protected]> Co-authored-by: Bert Droesbeke <[email protected]> Co-authored-by: Federico Bianchini <[email protected]>
elixir-europe · Dec 6, 2023 · 38427b5 · 38427b5
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diff --git a/_data/CONTRIBUTORS.yaml b/_data/CONTRIBUTORS.yaml
@@ -584,3 +584,18 @@ Diana Pilvar:
     orcid: 0000-0002-5788-2687
     affiliation: University of Tartu / ELIXIR-Estonia
     role: editor
+Johan Rollin:
+    git: johrollin
+    email: [email protected]
+    orcid: 0000-0002-9564-7872
+    affiliation: University of Freiburg / MeInBio program
+Mehmet Tekman:
+    git: mtekman
+    email: [email protected]
+    orcid: 0000-0002-4181-2676
+    affiliation: University of Freiburg / European Galaxy team
+Pavankumar Videm:
+    git: pavanvidem
+    email: [email protected]
+    orcid: 0000-0002-5192-126X
+    affiliation: University of Freiburg / European Galaxy team
diff --git a/_data/sidebars/data_management.yml b/_data/sidebars/data_management.yml
@@ -51,6 +51,8 @@ subitems:
         url: /proteomics
       - title: Rare disease data
         url: /rare_disease_data
+      - title: Single-cell sequencing
+        url: /single_cell_sequencing
       - title: Structural bioinformatics
         url: /structural_bioinformatics
       - title: Toxicology data

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
@@ -2297,3 +2297,90 @@
   registry:
     biotools: dataplan
   url: https://plan.nfdi4plants.org
+- description: Fast, sensitive and accurate integration of single-cell data.
+  id: harmony
+  name: Harmony
+  registry:
+    biotools: Harmony-R
+  url: https://github.com/immunogenomics/harmony
+- description: A database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data.
+  id: cellmarker
+  name: CellMarker
+  registry:
+    biotools: cellmarker_2.0
+  url: http://bio-bigdata.hrbmu.edu.cn/CellMarker/
+- description: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
+  id: seurat
+  name: Seurat
+  registry:
+    biotools: seurat
+  url: https://satijalab.org/seurat/
+- description: Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing.
+  id: scanpy
+  name: Scanpy
+  registry:
+    biotools: scanpy
+  url: https://github.com/theislab/Scanpy
+- description: The Gene Ontology Consortium continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences.
+  id: gene-ontology
+  name: Gene Ontology
+  registry:
+    biotools: go
+  url: http://www.geneontology.org/
+- description: Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray.
+  id: anndata
+  name: AnnData
+  url: https://anndata.readthedocs.io/en/latest/
+- description: Loom is an efficient file format for large omics datasets.
+  id: loom
+  name: Loom
+  url: https://loompy.org/
+- description: The main class used by Monocle to hold single cell expression data. CellDataSet extends the basic Bioconductor ExpressionSet class.
+  id: celldataset
+  name: CellDataSet
+  url: https://rdrr.io/bioc/monocle/man/CellDataSet.html
+- description: The SingleCellExperiment class is a lightweight Bioconductor container for storing and manipulating single-cell genomics data.
+  id: singlecellexperiment
+  name: SingleCellExperiment
+  url: https://www.bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html
+- description: The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
+  id: monocle
+  name: Monocle
+  registry:
+    biotools: monocle
+  url: https://cole-trapnell-lab.github.io/monocle3/
+- description: Scater offers a collection of tools for analysis (such as quality control) for single-cell gene expression data.
+  id: scater
+  name: Scater
+  url: https://bioconductor.org/packages/release/bioc/html/scater.html
+- description: sceasy is a package that helps easy conversion of different single-cell data formats to each other.
+  id: sceasy
+  name: SCEasy
+  url: https://github.com/cellgeni/sceasy
+- description:  Interactive portal for single-cell genomics data.
+  id: single-cell-portal
+  name: Single Cell Portal
+  url: https://singlecell.broadinstitute.org/single_cell
+- description: An entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
+  id: single-cell-best-pratices
+  name: Single-cell best pratices
+  url: https://www.sc-best-practices.org/preamble.html
+- description: A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.
+  id: cellranger
+  name: CellRanger 
+  url: https://www.10xgenomics.com/support/software/cell-ranger
+- description: A comprehensive turnkey solution for quantifying gene expression in single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR.
+  id: starsolo
+  name: STARsolo
+  url: https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md
+- description: HDF5 consists of a file format for storing HDF5 data, a data model for logically organizing and accessing HDF5 data from an application, and the software (libraries, language interfaces, and tools) for working with this format.
+  id: hierarchical-data-format 
+  name: Hierarchical Data Format 
+  url: https://www.10xgenomics.com/support/software/cell-ranger/analysis/outputs/cr-outputs-h5-matrices
+- description: Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data.
+  id: sequence-read-archive 
+  name: Sequence Read Archive 
+  url: https://www.ncbi.nlm.nih.gov/sra
+  registry:
+    fairsharing: g7t2hv
+