Alternatives and similar repositories for scater

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

• bvieth / powsimR
  Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially ex…
  ☆106Updated last year
• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆59Updated last week
• drisso / SingleCellExperiment
  Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCe…
  ☆72Updated last month
• YosefLab / scone
  ☆53Updated 3 months ago
• davismcc / archive-scater
  An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
  ☆64Updated 7 years ago
• rnabioco / clustifyr
  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
  ☆123Updated last month
• iaconogi / bigSCale2
  Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
  ☆104Updated last year
• GreenleafLab / chromVAR
  chromatin Variability Across Regions (of the genome!)
  ☆174Updated 10 months ago
• JEFworks-Lab / HoneyBADGER
  HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
  ☆97Updated 3 years ago
• niaid / dsb
  Normalize CITEseq Data
  ☆65Updated last month
• compbiomed / singleCellTK
  Interactively analyze single cell genomic data
  ☆182Updated 3 weeks ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆56Updated 8 months ago
• indrops / indrops
  Pipeline for processing inDrops sequencing data
  ☆76Updated 6 years ago
• hemberg-lab / scmap
  A tool for unsupervised projection of single cell RNA-seq data
  ☆96Updated 4 years ago
• PeeperLab / Rtoolbox
  Toolbox with R scripts
  ☆38Updated 6 years ago
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆90Updated 5 months ago
• rcannood / SCORPIUS
  Linear trajectory inference for single-cell RNA-seq
  ☆59Updated last year
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆76Updated 2 months ago
• LTLA / SingleCellThoughts
  Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.
  ☆44Updated 4 years ago
• kevinblighe / scDataviz
  scDataviz: single cell dataviz and downstream analyses
  ☆63Updated 3 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• sansomlab / tenx
  Pipelines for the analysis of 10x single-cell RNA-sequencing data
  ☆59Updated last year
• kevinrue / velociraptor
  Toolkit for Single-Cell Velocity
  ☆56Updated 5 months ago
• elimereu / matchSCore2
  ☆55Updated 4 years ago
• GIS-SP-Group / RCA
  R package for robust clustering of single cell RNA sequencing data
  ☆39Updated last year
• andygxzeng / BoneMarrowMap
  A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic …
  ☆55Updated last week
• csoneson / ARMOR
  Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
  ☆165Updated 5 months ago
• jokergoo / rGREAT
  GREAT Analysis - Functional Enrichment on Genomic Regions
  ☆87Updated 2 months ago
• wjawaid / enrichR
  An R interface to enrichR
  ☆92Updated 4 months ago
• mojaveazure / loomR
  An R-based interface for loom files
  ☆66Updated 4 years ago