Alternatives and similar repositories for signac

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

• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆340Updated 8 months ago
• cole-trapnell-lab / monocle3
  ☆396Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆424Updated 5 months ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆483Updated 4 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆343Updated this week
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆417Updated last week
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆630Updated 6 months ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆389Updated 2 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆558Updated last week
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆300Updated 5 years ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆289Updated 2 years ago
• Teichlab / cellphonedb
  ☆356Updated 3 years ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆423Updated 3 weeks ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆434Updated last year
• 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.
  ☆268Updated this week
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆227Updated 3 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆586Updated 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
• IanevskiAleksandr / sc-type
  ☆271Updated 8 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆438Updated last month
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆298Updated last year
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆498Updated 3 weeks ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆328Updated this week
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆382Updated 2 weeks ago
• cole-trapnell-lab / monocle-release
  ☆289Updated 3 years ago
• statOmics / tradeSeq
  TRAjectory-based Differential Expression analysis for SEQuencing data
  ☆276Updated last month
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆284Updated 2 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆291Updated 2 weeks ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆285Updated 2 years ago