Alternatives and similar repositories for single-cell-bioinformatics

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

• drisso / bioc2016singlecell
  Bioconductor workshop: Analysis of single-cell RNA-seq data with R and Bioconductor
  ☆80Updated 9 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.
  ☆104Updated 3 years ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆148Updated 2 years ago
• mskcc / RNAseqDB
  ☆142Updated 7 years ago
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆182Updated last year
• hms-dbmi / scde
  R package for analyzing single-cell RNA-seq data
  ☆177Updated last year
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated 2 years ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆97Updated 6 years ago
• mgonzalezporta / TeachingMaterial
  RNA-seq data analysis practical
  ☆60Updated 11 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-…
  ☆106Updated 3 years ago
• crazyhottommy / papers_with_data_to_mine
  published papers with a lot of data
  ☆74Updated 8 months ago
• tallulandrews / scRNASeqPipeline
  ☆118Updated 7 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
• GreenleafLab / NucleoATAC
  nucleosome calling using ATAC-seq
  ☆109Updated 4 years ago
• statgen / demuxlet
  Genetic multiplexing of barcoded single cell RNA-seq
  ☆131Updated last year
• crazyhottommy / pyflow-ATACseq
  ATAC-seq snakemake pipeline
  ☆88Updated 5 years ago
• sansomlab / tenx
  Pipelines for the analysis of 10x single-cell RNA-sequencing data
  ☆58Updated 2 years ago
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆132Updated 2 years ago
• mdozmorov / Cancer_notes
  A continually expanding collection of cancer genomics notes and data
  ☆110Updated last month
• ENCODE-DCC / long-rna-seq-pipeline
  STAR based ENCODE Long RNA-Seq processing pipeline
  ☆96Updated 4 years ago
• hdng / clonevol
  Inferring and visualizing clonal evolution in multi-sample cancer sequencing
  ☆148Updated 5 years ago
• PoisonAlien / TCGAmutations
  R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE
  ☆98Updated last year
• reimandlab / ActivePathways
  Integrative pathway enrichment analysis of multivariate omics data
  ☆117Updated 4 months ago
• iaconogi / bigSCale2
  Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
  ☆107Updated 2 years ago
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆132Updated last year
• BaderLab / CellAnnotationTutorial
  Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods
  ☆97Updated 2 years ago
• indrops / indrops
  Pipeline for processing inDrops sequencing data
  ☆76Updated 7 years ago
• timoast / sinto
  Tools for single-cell data processing
  ☆128Updated last year