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
  ☆464Updated last month
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆419Updated 2 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆331Updated 5 months ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆611Updated 3 months ago
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆369Updated 4 months ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆536Updated this week
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆412Updated last week
• Teichlab / cellphonedb
  ☆355Updated 3 years ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆295Updated 4 years ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆326Updated 10 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆495Updated 11 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆398Updated last month
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆332Updated last week
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆573Updated 6 months ago
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆422Updated last year
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆224Updated 2 weeks ago
• smorabit / hdWGCNA
  High dimensional weighted gene co-expression network analysis
  ☆405Updated last month
• navinlabcode / copykat
  ☆233Updated 10 months ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆317Updated 2 years ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆323Updated this week
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆374Updated 5 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆276Updated 2 years ago
• IanevskiAleksandr / sc-type
  ☆262Updated 6 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆486Updated last week
• cole-trapnell-lab / monocle-release
  ☆286Updated 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.
  ☆253Updated 3 weeks ago
• dmcable / spacexr
  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial …
  ☆363Updated 11 months ago
• aertslab / SCENIC
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
  ☆447Updated last year
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆273Updated this week
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆291Updated last year