Alternatives and similar repositories for HLCA

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

• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆81Updated 8 months ago
• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆57Updated 2 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆91Updated 6 months ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆76Updated last year
• xleizi / easySCF
  ☆48Updated last month
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆97Updated 11 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆67Updated last month
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆57Updated last week
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆81Updated 3 years ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆90Updated 3 months ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆45Updated 3 weeks ago
• cellgeni / batchbench
  ☆46Updated 3 years ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆60Updated 3 years ago
• Nanostring-Biostats / SpatialDecon
  The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This al…
  ☆41Updated 6 months ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆112Updated last month
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆80Updated 10 months ago
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆81Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆88Updated last month
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆115Updated last year
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆29Updated last year
• linnarsson-lab / developing-human-brain
  ☆36Updated last month
• matanhofree / crc-immune-hubs
  Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…
  ☆38Updated 4 years ago
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• buenrostrolab / stimATAC_analyses_code
  All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
  ☆41Updated 2 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆105Updated last year
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆66Updated 3 months ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆90Updated 5 months ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆77Updated 4 months ago
• quadbio / Pando
  Multiome GRN inference.
  ☆131Updated last year