Alternatives and similar repositories for leiden

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

• stephenslab / fastTopics
  Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
  ☆84Updated 3 weeks ago
• willtownes / glmpca
  ☆96Updated last year
• cole-trapnell-lab / leidenbase
  ☆13Updated 9 months ago
• Shians / CellBench
  R package for benchmarking single cell analysis methods
  ☆32Updated 2 years ago
• dynverse / dynplot
  Visualising single-cell trajectories, including comparisons between two models 📈
  ☆32Updated 4 years ago
• SaskiaFreytag / schex
  ☆75Updated last year
• RTCGA / RTCGA
  Download, integration and visualizations of the variety & volume of TCGA data.
  ☆51Updated 3 years ago
• tidyomics / tidySingleCellExperiment
  Brings SingleCellExperiment objects to the tidyverse
  ☆37Updated 2 months ago
• milescsmith / ReductionWrappers
  R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)
  ☆36Updated last year
• Bioconductor / BiocParallel
  Bioconductor facilities for parallel evaluation
  ☆69Updated 2 months ago
• linxihui / NNLM
  Nonnegative Linear Models (NNLM) and Nonnegative Matrix Factorization (NMF or NNMF).
  ☆82Updated last year
• renozao / NMF
  NMF: A Flexible R package for Nonnegative Matrix Factorization
  ☆152Updated 2 years ago
• anders-biostat / sleepwalk
  Exploring dimension-reduced embeddings
  ☆111Updated 3 years ago
• LTLA / basilisk
  Clone of the Bioconductor repository for the basilisk package.
  ☆29Updated 2 months ago
• GabrielHoffman / variancePartition
  Quantify and interpret divers of variation in multilevel gene expression experiments
  ☆69Updated last month
• SingleR-inc / SingleRBook-base
  See https://github.com/LTLA/SingleRBook for the latest version of this content.
  ☆12Updated 3 years ago
• mw201608 / SuperExactTest
  Statistical testing and visualization of mult-set intersections
  ☆29Updated 2 years ago
• goncalves-lab / waddR
  R package for detecting differential distributions using a statistical test based on the wasserstein distance
  ☆27Updated 2 months ago
• mararie / lionessR
  Single sample network reconstruction in R
  ☆24Updated 5 years ago
• jokergoo / cola
  A General Framework for Consensus Partitioning
  ☆65Updated 11 months ago
• yanwu2014 / swne
  Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
  ☆106Updated 2 years ago
• Sage-Bionetworks / synapser
  An R package providing programmatic access to Synapse
  ☆37Updated this week
• federicomarini / pcaExplorer
  pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
  ☆56Updated last month
• kstreet13 / scry
  Collection of analysis methods for small count data generated by rafalab members (the methods, not the data).
  ☆22Updated last year
• myles-lewis / glmmSeq
  Gene-level general linear mixed model
  ☆24Updated 3 months ago
• ropensci / UCSCXenaTools
  An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.…
  ☆111Updated 3 months ago
• epurdom / clusterExperiment
  R package of techniques for comparing clusterings of single-cell sequencing data
  ☆40Updated last year
• crj32 / M3C
  Monte Carlo Reference-based Consensus Clustering
  ☆36Updated 5 years ago
• Bioconductor / OrchestratingSingleCellAnalysis-release
  An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.
  ☆37Updated 2 years ago
• kevinblighe / RegParallel
  Standard regression functions in R enabled for parallel processing over large data-frames.
  ☆38Updated 2 years ago