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
  ☆291Updated 2 years ago
• SingleR-inc / SingleR
  Clone of the Bioconductor repository for the SingleR package.
  ☆193Updated 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.
  ☆269Updated this week
• navinlabcode / copykat
  ☆247Updated last year
• RGLab / MAST
  Tools and methods for analysis of single cell assay data in R
  ☆249Updated last year
• BorchLab / scRepertoire
  A toolkit for single-cell immune profiling
  ☆345Updated 2 weeks ago
• dviraran / SingleR
  SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
  ☆302Updated 5 years ago
• neurorestore / Libra
  ☆174Updated 3 months ago
• MarioniLab / miloR
  R package implementation of Milo for testing for differential abundance in KNN graphs
  ☆391Updated 2 months ago
• plger / scDblFinder
  Methods for detecting doublets in single-cell sequencing data
  ☆205Updated 2 weeks ago
• HelenaLC / muscat
  Multi-sample multi-group scRNA-seq analysis tools
  ☆197Updated 3 months ago
• welch-lab / liger
  R package for integrating and analyzing multiple single-cell datasets
  ☆419Updated this week
• satijalab / seurat-wrappers
  Community-provided extensions to Seurat
  ☆342Updated 9 months ago
• rcastelo / GSVA
  Gene set variation analysis
  ☆224Updated 4 months ago
• kharchenkolab / pagoda2
  R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
  ☆234Updated last week
• kstreet13 / slingshot
  Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
  ☆304Updated last year
• velocyto-team / velocyto.R
  RNA velocity estimation in R
  ☆188Updated last year
• basilkhuder / Seurat-to-RNA-Velocity
  A guide to using a Seurat object in conjunction with RNA Velocity
  ☆139Updated 3 years ago
• ZJUFanLab / scCATCH
  Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
  ☆231Updated 2 years ago
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆353Updated 3 weeks ago
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated this week
• SGDDNB / ShinyCell
  Shiny Interactive Web Apps for Single-Cell Data
  ☆193Updated 4 months ago
• xuranw / MuSiC
  Multi-subject Single Cell Deconvolution
  ☆268Updated last year
• satijalab / seurat-data
  Dataset distribution for Seurat
  ☆143Updated 5 months ago
• immunogenomics / presto
  Fast Wilcoxon and auROC
  ☆187Updated 9 months ago
• carmonalab / ProjecTILs
  Interpretation of cell states using reference single-cell maps
  ☆290Updated 2 weeks ago
• mojaveazure / seurat-disk
  Interfaces for HDF5-based Single Cell File Formats
  ☆167Updated last year
• huayc09 / SeuratExtend
  ☆163Updated last week
• enblacar / SCpubr
  Generate high quality, publication ready visualizations for single cell transcriptomics data.
  ☆206Updated 2 weeks ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆289Updated 2 years ago