Alternatives and similar repositories for ArchR

Users that are interested in ArchR are comparing it to the libraries listed below

• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆514Updated 8 months ago
• cole-trapnell-lab / monocle3
  ☆424Updated 2 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆351Updated last year
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆356Updated last week
• Teichlab / cellphonedb
  ☆359Updated 4 years ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆398Updated last week
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆420Updated last month
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆313Updated 5 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆321Updated 2 years ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆598Updated last month
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆365Updated 4 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆448Updated last year
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆645Updated last month
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆404Updated 3 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆301Updated 3 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆333Updated this week
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆450Updated last month
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆486Updated 6 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆502Updated 2 months ago
• IanevskiAleksandr / sc-type
  ☆279Updated last year
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆472Updated last year
• navinlabcode / copykat
  ☆259Updated 2 months ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆242Updated 7 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆511Updated last month
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆318Updated 2 years ago
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆437Updated last week
• cole-trapnell-lab / monocle-release
  ☆291Updated 3 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆296Updated 2 years ago
• samuel-marsh / scCustomize
  R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆282Updated this week
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆318Updated last year