Alternatives and similar repositories for scRNA-tools

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

• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆343Updated last week
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆300Updated 5 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆417Updated last week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆291Updated 3 weeks ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆424Updated 5 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆281Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆309Updated 2 years ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆340Updated 8 months ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆226Updated 3 years ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆472Updated 2 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆227Updated 3 months ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆285Updated 2 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆289Updated 2 years ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆220Updated 3 months ago
• cole-trapnell-lab / monocle-release
  ☆289Updated 3 years ago
• hbctraining / Intro-to-DGE
  ☆205Updated 4 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆498Updated 3 weeks ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆558Updated last week
• IanevskiAleksandr / sc-type
  ☆271Updated 8 months ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆425Updated 5 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆383Updated 2 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆483Updated 4 months ago
• Teichlab / cellphonedb
  ☆356Updated 3 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆261Updated 8 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆343Updated last year
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆271Updated last year
• immunomind / immunarch
  🧬 immunarch [R package] – Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
  ☆323Updated last year
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆246Updated last year