Alternatives and similar repositories for HLCA

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

• LungCellAtlas / HLCA_reproducibility
  This repository contains all code used for the Human Lung Cell Atlas project.
  ☆51Updated last year
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆85Updated 2 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆83Updated 7 months ago
• JEFworks-Lab / MERINGUE
  characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular dens…
  ☆77Updated 3 years ago
• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆75Updated 11 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆79Updated 4 months ago
• xleizi / easySCF
  ☆43Updated last month
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆43Updated 3 weeks ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆63Updated this week
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆86Updated 2 months ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆120Updated last week
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆73Updated 3 weeks ago
• KlugerLab / DAseq
  ☆41Updated 4 years ago
• immunogenomics / symphony
  Efficient and precise single-cell reference atlas mapping with Symphony
  ☆105Updated 2 years ago
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆55Updated 3 months ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆59Updated 3 years ago
• CostaLab / scMEGA
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
  ☆40Updated 10 months ago
• 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…
  ☆39Updated 3 years ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆63Updated 3 years ago
• buenrostrolab / stimATAC_analyses_code
  All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs
  ☆41Updated 2 years ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆86Updated last month
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆28Updated 8 months ago
• cailab-tamu / scTenifoldKnk
  R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.
  ☆59Updated 7 months ago
• pachterlab / LP_2021
  ☆49Updated last month
• livnatje / DIALOGUE
  DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…
  ☆113Updated last year
• quadbio / Pando
  Multiome GRN inference.
  ☆124Updated last year
• saezlab / progeny
  R package for Pathway RespOnsive GENe activity inference
  ☆106Updated 2 years ago
• cellgeni / batchbench
  ☆47Updated 3 years ago
• abelson-lab / scATOMIC
  Pan-Cancer Single Cell Classifier
  ☆74Updated last year
• data2intelligence / CytoSig
  ☆55Updated 10 months ago