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)
  ☆76Updated 2 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆149Updated this week
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆52Updated 2 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆97Updated 8 months ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆92Updated last month
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆100Updated this week
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆138Updated 6 months ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆95Updated last week
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆93Updated last year
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated 2 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆85Updated 10 months ago
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆86Updated 2 months ago
• theislab / destiny
  R package for single cell and other data analysis using diffusion maps
  ☆92Updated 2 months ago
• nimwegenLab / cellstates
  Finding gene expression states in scRNA-seq data
  ☆50Updated last year
• crazyhottommy / scclusteval
  Single Cell Cluster Evaluation
  ☆99Updated 4 years ago
• tanaylab / metacell
  Metacell - Single-cell mRNA Analysis
  ☆120Updated last year
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆113Updated 3 months ago
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆114Updated 3 years ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆104Updated last month
• niaid / dsb
  Normalize CITEseq Data
  ☆67Updated 3 months ago
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆35Updated 3 weeks ago
• lhe17 / nebula
  ☆48Updated 2 months ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆66Updated 2 years ago
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆57Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 8 months ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆45Updated last week
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆106Updated last year
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆60Updated 3 years ago
• rnabioco / clustifyr
  Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
  ☆125Updated 9 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆69Updated 3 months ago