Alternatives and similar repositories for scRNA-tools

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

• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆306Updated 5 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆320Updated 2 years ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆353Updated last week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆297Updated last week
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆286Updated last year
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆422Updated last month
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆224Updated last month
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆293Updated 2 years ago
• Teichlab / cellphonedb
  ☆360Updated 3 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆296Updated 2 years ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆315Updated 2 years ago
• IanevskiAleksandr / sc-type
  ☆275Updated 11 months ago
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆433Updated 8 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆348Updated 11 months ago
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆226Updated 3 years ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆240Updated 5 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆506Updated 2 weeks ago
• cole-trapnell-lab / monocle-release
  ☆289Updated 3 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆266Updated 10 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆483Updated 5 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆384Updated last month
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆132Updated last year
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆434Updated 8 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆578Updated last week
• navinlabcode / copykat
  ☆256Updated last week
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆152Updated 3 years ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆324Updated 4 years ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆393Updated 2 weeks ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆501Updated 7 months ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆274Updated last year