Alternatives and similar repositories for single-cell-bioinformatics

Users that are interested in single-cell-bioinformatics are comparing it to the libraries listed below

• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• snakemake-workflows / single-cell-rna-seq
  A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.
  ☆103Updated 2 years ago
• mskcc / RNAseqDB
  ☆142Updated 7 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆181Updated last year
• hms-dbmi / scde
  R package for analyzing single-cell RNA-seq data
  ☆176Updated last year
• drisso / bioc2016singlecell
  Bioconductor workshop: Analysis of single-cell RNA-seq data with R and Bioconductor
  ☆80Updated 8 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆95Updated 6 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆108Updated 4 years ago
• nsalomonis / altanalyze
  AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-…
  ☆105Updated 3 years ago
• reimandlab / ActivePathways
  Integrative pathway enrichment analysis of multivariate omics data
  ☆115Updated 3 months ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆148Updated 2 years ago
• mgonzalezporta / TeachingMaterial
  RNA-seq data analysis practical
  ☆60Updated 11 years ago
• crazyhottommy / papers_with_data_to_mine
  published papers with a lot of data
  ☆74Updated 6 months ago
• indrops / indrops
  Pipeline for processing inDrops sequencing data
  ☆76Updated 7 years ago
• mdozmorov / Cancer_notes
  A continually expanding collection of cancer genomics notes and data
  ☆108Updated last week
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆88Updated 5 years ago
• jdblischak / singleCellSeq
  Batch effects and the effective design of single-cell gene expression studies
  ☆104Updated 6 years ago
• tavareshugo / tutorial_DESeq2_contrasts
  ☆63Updated last year
• sansomlab / tenx
  Pipelines for the analysis of 10x single-cell RNA-sequencing data
  ☆58Updated 2 years ago
• riazn / bms038_analysis
  Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for man…
  ☆51Updated 7 years ago
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆130Updated last year
• PoisonAlien / TCGAmutations
  R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE
  ☆98Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆127Updated last year
• chrisamiller / fishplot
  Create timecourse "fish plots" that show changes in the clonal architecture of tumors
  ☆171Updated 2 years ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 years ago
• Teichlab / embl-single-cell-course-2016
  Material for lecture at the EMBL Single Cell Course 2016
  ☆47Updated 9 years ago
• srp33 / TCGA_RNASeq_Clinical
  ☆62Updated 5 years ago
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago
• TrinityCTAT / Trinity_CTAT
  ☆120Updated 2 years ago