Alternatives and similar repositories for scRNA-seq-pipelines

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

• elimereu / matchSCore2
  ☆55Updated 4 years ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• willtownes / scrna2019
  supporting code for the multinomial single cell RNA-Seq paper
  ☆52Updated 4 years ago
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆50Updated last year
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• icbi-lab / immune_deconvolution_benchmark
  Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…
  ☆43Updated 5 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆79Updated 8 months ago
• crazyhottommy / scATACutils
  R/Bioconductor package for working with 10x scATACseq data
  ☆42Updated 2 years ago
• GIS-SP-Group / RCA
  R package for robust clustering of single cell RNA sequencing data
  ☆40Updated 2 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆47Updated 2 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆81Updated 3 years ago
• ParkerLab / bioinf545
  ATAC-seq lab for BIOINF545
  ☆24Updated 8 months ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆57Updated 4 years ago
• JunyueC / sci-RNA-seq3_pipeline
  Processing pipeline scripts for sci-RNA-seq3 (bash, R, python)
  ☆43Updated 4 years ago
• shenorrLabTRDF / bseqsc
  Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline
  ☆46Updated 2 years ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆52Updated 2 years ago
• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 3 years ago
• MarioniLab / EmbryoTimecourse2018
  Data and analysis scripts for our Embryo Timecourse paper.
  ☆69Updated 5 years ago
• single-cell-genetics / cardelino
  Clone identification from single-cell data
  ☆61Updated 3 years ago
• JEFworks / MUDAN
  Multi-sample Unified Discriminant ANalysis
  ☆74Updated 2 years ago
• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆62Updated 2 months ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆42Updated 4 years ago
• pachterlab / kallisto-transcriptome-indices
  Reference transcriptome indices build from kallisto for popular organisms
  ☆44Updated last year
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆75Updated 4 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…
  ☆41Updated 2 years ago
• Neurosurgery-Brain-Tumor-Center-DiazLab / CONICS
  CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
  ☆75Updated 2 years ago