Alternatives and similar repositories for immunarch

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

• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆362Updated last week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆309Updated 3 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆425Updated this week
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆338Updated this week
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆273Updated last year
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆199Updated last month
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆433Updated last month
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆248Updated 3 weeks ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆355Updated last week
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆321Updated 5 years ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆309Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆445Updated 11 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆322Updated 2 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆300Updated 2 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆311Updated 3 years ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆411Updated 5 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆520Updated last month
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆324Updated last year
• statOmics / tradeSeq
  TRAjectory-based Differential Expression analysis for SEQuencing data
  ☆287Updated 7 months ago
• hbctraining / Intro-to-DGE
  ☆211Updated 5 months ago
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆284Updated last year
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆338Updated 2 weeks ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆465Updated last month
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆290Updated last year
• IanevskiAleksandr / sc-type
  ☆285Updated last year
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆403Updated 3 weeks ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆236Updated last month
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆260Updated 3 months ago
• cole-trapnell-lab / monocle3
  ☆437Updated last month
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆614Updated 2 months ago