Alternatives and similar repositories for monocle3

Users that are interested in monocle3 are comparing it to the libraries listed below

• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆513Updated 8 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆399Updated this week
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆351Updated last year
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆438Updated 9 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆420Updated last month
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆596Updated 3 weeks ago
• Teichlab / cellphonedb
  ☆359Updated 4 years ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆497Updated 2 months ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆449Updated last month
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆311Updated 5 years ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆647Updated 3 weeks ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆472Updated last year
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆355Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆448Updated last year
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆403Updated 3 months ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆315Updated last year
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆614Updated 2 months ago
• IanevskiAleksandr / sc-type
  ☆277Updated last year
• navinlabcode / copykat
  ☆258Updated last month
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆366Updated 4 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆300Updated 3 years ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆511Updated last month
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆242Updated 7 months ago
• cole-trapnell-lab / monocle-release
  ☆290Updated 3 years ago
• quadbio / scRNAseq_analysis_vignette
  Tutorial for scRNA-seq data analysis beginners using R
  ☆233Updated 9 months ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆419Updated 4 months 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.
  ☆280Updated this week
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆321Updated 2 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆333Updated this week
• junjunlab / scRNAtoolVis
  Useful functions to make your scRNA-seq plot more cool!
  ☆366Updated 6 months ago