Alternatives and similar repositories for BASiCS

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

• nghiavtr / ISOP

  View on GitHub
  Isoform-level expression patterns in single-cell RNA-sequencing data
  ☆11Apr 20, 2023Updated 2 years ago
• PMBio / scLVM

  View on GitHub
  scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…
  ☆110Dec 16, 2022Updated 3 years ago
• Oshlack / splatter

  View on GitHub
  Simple simulation of single-cell RNA sequencing data
  ☆234Jan 12, 2026Updated last month
• kieranrcampbell / ouijaflow

  View on GitHub
  Probabilistic single-cell pseudotime with Edward+Tensorflow
  ☆12Oct 5, 2017Updated 8 years ago
• compbiomed / celda

  View on GitHub
  Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data
  ☆48May 3, 2019Updated 6 years ago
• single-cell-genetics / cardelino

  View on GitHub
  Clone identification from single-cell data
  ☆61Nov 10, 2022Updated 3 years ago
• MarioniLab / scran

  View on GitHub
  Clone of the Bioconductor repository for the scran package.
  ☆46Sep 5, 2024Updated last year
• theislab / graph_abstraction

  View on GitHub
  Generate cellular maps of differentiation manifolds with complex topologies.
  ☆27Jun 26, 2018Updated 7 years ago
• kdkorthauer / scDD

  View on GitHub
  R package to identify genes with differential distributions in single-cell RNA-seq
  ☆34Mar 24, 2022Updated 3 years ago
• bioFAM / slalom

  View on GitHub
  ☆29Feb 1, 2023Updated 3 years ago
• mtmorgan / TENxGenomics

  View on GitHub
  Interface to 10x Genomics' 1.3 m single cell data set
  ☆18Aug 2, 2018Updated 7 years ago
• vals / umis

  View on GitHub
  Tools for processing UMI RNA-tag data
  ☆131Mar 15, 2023Updated 2 years ago
• pachterlab / scRNA-Seq-TCC-prep

  View on GitHub
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Jul 5, 2019Updated 6 years ago
• Shians / BiocExplorer

  View on GitHub
  ☆11Sep 5, 2018Updated 7 years ago
• COMBINE-lab / wasabi

  View on GitHub
  Prepare Sailfish and Salmon output for downstream analysis
  ☆42Jun 6, 2019Updated 6 years ago
• willtownes / scrna2019

  View on GitHub
  supporting code for the multinomial single cell RNA-Seq paper
  ☆53Jan 6, 2021Updated 5 years ago
• markrobinsonuzh / scRNAseq_clustering_comparison

  View on GitHub
  A study to compare methods for clustering of scRNA-seq data
  ☆45Jul 19, 2024Updated last year
• talgalili / dendextendRcpp

  View on GitHub
  Faster manipulation of dendrogram objects in R.
  ☆15May 22, 2015Updated 10 years ago
• xzhoulab / DRComparison

  View on GitHub
  Comparison of dimensionality reduction methods
  ☆30Mar 24, 2020Updated 5 years ago
• govinda-kamath / clustering_on_transcript_compatibility_counts

  View on GitHub
  Clustering cells from single cell RNA seq assays
  ☆46Nov 19, 2018Updated 7 years ago
• bvieth / powsimR

  View on GitHub
  Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially ex…
  ☆107Aug 1, 2023Updated 2 years ago
• alanocallaghan / scater

  View on GitHub
  Clone of the Bioconductor repository for the scater package.
  ☆95Jan 12, 2026Updated last month
• theislab / kBET

  View on GitHub
  An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.
  ☆169Jan 26, 2024Updated 2 years ago
• SaskiaFreytag / schex

  View on GitHub
  ☆75Feb 4, 2024Updated 2 years ago
• kharchenkolab / conos

  View on GitHub
  R package for the joint analysis of multiple single-cell RNA-seq datasets
  ☆218Feb 26, 2024Updated last year
• yanwu2014 / swne

  View on GitHub
  Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
  ☆107Aug 2, 2023Updated 2 years ago
• kieranrcampbell / ouija

  View on GitHub
  Descriptive probabilistic marker gene approach to single-cell pseudotime inference
  ☆31Nov 29, 2019Updated 6 years ago
• cz-ye / DECENT

  View on GitHub
  Differential Expression with Capture Efficiency adjustmeNT
  ☆15Jan 3, 2023Updated 3 years ago
• Bioconductor / BiocStyle

  View on GitHub
  Issues and pull requests for BiocStyle should go here.
  ☆14Oct 30, 2025Updated 3 months ago
• epurdom / clusterExperiment

  View on GitHub
  R package of techniques for comparing clusterings of single-cell sequencing data
  ☆41Apr 26, 2024Updated last year
• markrobinsonuzh / conquer

  View on GitHub
  consistent quantification of external RNA-seq data sets
  ☆58Dec 21, 2023Updated 2 years ago
• immunogenomics / cna

  View on GitHub
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Jun 1, 2025Updated 8 months ago
• drisso / SingleCellExperiment

  View on GitHub
  Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCe…
  ☆75Jun 30, 2025Updated 7 months ago
• shazanfar / scHOT

  View on GitHub
  ☆11May 30, 2023Updated 2 years ago
• kieranrcampbell / phenopath

  View on GitHub
  Genomic trajectories (pseudotimes) in the presence of heterogenous environmental and genetic backgrounds
  ☆12Mar 21, 2019Updated 6 years ago
• hms-dbmi / scde

  View on GitHub
  R package for analyzing single-cell RNA-seq data
  ☆179Feb 29, 2024Updated last year
• AllonKleinLab / SPRING

  View on GitHub
  ☆69May 2, 2018Updated 7 years ago
• dcjones / isolator

  View on GitHub
  Rapid and robust analysis of RNA-Seq experiments.
  ☆32Apr 16, 2016Updated 9 years ago
• davismcc / archive-scater

  View on GitHub
  An archived version of the scater repository, see https://github.com/davismcc/scater for the active version.
  ☆64Sep 4, 2017Updated 8 years ago