Alternatives and similar repositories for lemur

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

• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆72Updated last year
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆87Updated 4 months ago
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆52Updated last year
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆97Updated 2 weeks ago
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆92Updated 9 months ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆89Updated 3 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆115Updated this week
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆124Updated 2 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆90Updated last month
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆85Updated last year
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated 5 months ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆108Updated 2 years ago
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆79Updated last year
• MangiolaLaboratory / sccomp
  Mixed-effect model to test differences in cell type proportions from single-cell data, in R
  ☆111Updated 2 weeks ago
• niaid / dsb
  Normalize CITEseq Data
  ☆66Updated 5 months ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆64Updated last year
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 6 months ago
• vertesy / Seurat.utils
  Various utility functions for Seurat single-cell analysis
  ☆53Updated 2 weeks ago
• nimwegenLab / cellstates
  Finding gene expression states in scRNA-seq data
  ☆51Updated last year
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆97Updated 4 years ago
• theislab / destiny
  R package for single cell and other data analysis using diffusion maps
  ☆88Updated 10 months ago
• rnabioco / clustifyr
  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
  ☆124Updated 5 months ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆110Updated 2 years ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆59Updated 3 years ago
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆75Updated 4 years ago
• timoast / sinto
  Tools for single-cell data processing
  ☆127Updated last year
• igrabski / sc-SHC
  Significance analysis for clustering single-cell RNA-sequencing data
  ☆119Updated last year
• tanaylab / metacell
  Metacell - Single-cell mRNA Analysis
  ☆117Updated 8 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆104Updated last year