Alternatives and similar repositories for slingshot:

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

• satijalab / sctransform
  R package for modeling single cell UMI expression data using regularized negative binomial regression
  ☆220Updated 2 months ago
• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆264Updated 2 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆183Updated this week
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆355Updated 3 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.
  ☆242Updated 2 weeks ago
• saezlab / liana
  LIANA: a LIgand-receptor ANalysis frAmework
  ☆192Updated 6 months ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆326Updated last week
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆180Updated last week
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆263Updated 3 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆223Updated last year
• statOmics / tradeSeq
  TRAjectory-based Differential Expression analysis for SEQuencing data
  ☆247Updated 3 weeks ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆181Updated this week
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆402Updated last month
• neurorestore / Libra
  ☆162Updated 5 months ago
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆222Updated 11 months ago
• satijalab / seurat-data
  Dataset distribution for Seurat
  ☆135Updated last year
• navinlabcode / copykat
  ☆225Updated 7 months ago
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆321Updated 2 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆306Updated 7 months ago
• Oshlack / splatter
  Simple simulation of single-cell RNA sequencing data
  ☆224Updated 2 months ago
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆155Updated last year
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆231Updated last year
• Dragonmasterx87 / Interactive-3D-Plotting-in-Seurat-3.0.0
  This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data
  ☆121Updated last year
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆311Updated last year
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆282Updated 4 years ago
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆513Updated this week
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆245Updated 11 months ago
• theislab / zellkonverter
  Conversion between scRNA-seq objects
  ☆159Updated 2 months ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆181Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆406Updated 11 months ago