Alternatives and similar repositories for sctransform

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

• constantAmateur / SoupX
  R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
  ☆311Updated 3 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆199Updated last month
• 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.
  ☆287Updated last week
• navinlabcode / copykat
  ☆269Updated 3 months ago
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆260Updated 3 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆230Updated last month
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆324Updated last year
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆246Updated 5 months ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆411Updated 5 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆425Updated this week
• statOmics / tradeSeq
  TRAjectory-based Differential Expression analysis for SEQuencing data
  ☆287Updated 7 months ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆320Updated 5 years ago
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆362Updated last week
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆217Updated last month
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆170Updated 2 years ago
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆284Updated last year
• velocyto-team / velocyto.R
  RNA velocity estimation in R
  ☆194Updated 2 years ago
• BorchLab / escape
  Easy single cell analysis platform for enrichment
  ☆209Updated last month
• rcastelo / GSVA
  Gene set variation analysis
  ☆231Updated last month
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆184Updated 3 weeks ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆309Updated last month
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆355Updated last week
• bnprks / BPCells
  Scaling Single Cell Analysis to Millions of Cells
  ☆257Updated 3 weeks ago
• neurorestore / Libra
  ☆181Updated 9 months ago
• immunogenomics / presto
  Fast Wilcoxon and auROC
  ☆204Updated last year
• satijalab / seurat-data
  Dataset distribution for Seurat
  ☆151Updated 11 months ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆237Updated 2 years ago
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆140Updated 4 years ago
• huayc09 / SeuratExtend
  ☆202Updated 2 months ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆375Updated 6 months ago