Alternatives and similar repositories for monocle-release

Users that are interested in monocle-release are comparing it to the libraries listed below

• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆307Updated 5 years ago
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆320Updated 2 years ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆421Updated 2 weeks ago
• Teichlab / cellphonedb
  ☆360Updated 3 years ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆294Updated 2 years ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆351Updated 11 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆297Updated 3 years ago
• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆241Updated 6 months ago
• scRNA-tools / scRNA-tools
  Table of software for the analysis of single-cell RNA-seq data.
  ☆332Updated this week
• navinlabcode / copykat
  ☆255Updated last month
• cole-trapnell-lab / monocle3
  ☆416Updated 2 months ago
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆257Updated last month
• NBISweden / excelerate-scRNAseq
  Single RNA-seq data analysis with R (Finland, May, 2019)
  ☆226Updated 3 years ago
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆311Updated last year
• GreenleafLab / ArchR
  ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
  ☆436Updated 9 months ago
• IanevskiAleksandr / sc-type
  ☆276Updated last year
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆194Updated 2 years ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆299Updated last month
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆197Updated last month
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆445Updated last year
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆354Updated last week
• stuart-lab / signac
  R toolkit for the analysis of single-cell chromatin data
  ☆395Updated last week
• crazyhottommy / scATACseq-analysis-notes
  my notes for scATACseq analysis
  ☆131Updated last year
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆234Updated 2 years ago
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆504Updated 7 months ago
• velocyto-team / velocyto.R
  RNA velocity estimation in R
  ☆190Updated 2 years ago
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆275Updated last year
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆511Updated 2 weeks ago
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆232Updated last week
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆286Updated last year