Alternatives and similar repositories for scRNA-seq-pipelines:

Users that are interested in scRNA-seq-pipelines are comparing it to the libraries listed below

• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• elimereu / matchSCore2
  ☆53Updated 4 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆74Updated last week
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆41Updated 4 years ago
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆45Updated last year
• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 2 years ago
• lanagarmire / SSrGE
  ☆33Updated 5 years ago
• YosefLab / ImpulseDE2
  ☆36Updated 2 years ago
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆48Updated last year
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆47Updated 3 years ago
• seasoncloud / Alleloscope
  Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separ…
  ☆29Updated 2 years ago
• qinqian / lisa
  epigenome analysis to rank transcription factors
  ☆30Updated 2 years ago
• single-cell-genetics / cardelino
  Clone identification from single-cell data
  ☆61Updated 2 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆58Updated 2 years ago
• jon-xu / scSplit
  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…
  ☆42Updated 2 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆43Updated last year
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆77Updated 2 years ago
• broadinstitute / 2019_scWorkshop
  Repo for Physalia course Analysis of Single Cell RNA-Seq data
  ☆31Updated 5 years ago
• andygxzeng / BoneMarrowMap
  A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic …
  ☆37Updated 4 months ago
• vivekbhr / Subread_to_DEXSeq
  Scripts to import your FeatureCounts output into DEXSeq
  ☆33Updated 6 years ago
• ParkerLab / ataqv
  A toolkit for QC and visualization of ATAC-seq results.
  ☆67Updated 2 months ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 4 years ago
• GIS-SP-Group / RCA
  R package for robust clustering of single cell RNA sequencing data
  ☆38Updated last year
• willtownes / scrna2019
  supporting code for the multinomial single cell RNA-Seq paper
  ☆51Updated 4 years ago
• cole-trapnell-lab / cicero-release
  ☆59Updated 6 months ago
• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆57Updated 3 months ago
• ParkerLab / bioinf545
  ATAC-seq lab for BIOINF545
  ☆25Updated last month
• cboix / EPIMAP_ANALYSIS
  Epimap processing and analysis code repository
  ☆33Updated 2 years ago
• databio / pepatac
  A modular, containerized pipeline for ATAC-seq data processing
  ☆55Updated 2 weeks ago
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆42Updated last year