Alternatives and similar repositories for scATOMIC

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

• jackbibby1 / SCPA
  R package for pathway analysis in scRNA-seq data
  ☆73Updated 9 months ago
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆81Updated 9 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆79Updated last week
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆111Updated last month
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆82Updated 3 weeks ago
• swaruplabUCI / ArchRtoSignac
  An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  ☆36Updated 9 months ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆68Updated 10 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆75Updated 2 months ago
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆65Updated 7 months ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆59Updated 3 years ago
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆95Updated last year
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆106Updated 2 months ago
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 4 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆101Updated 8 months ago
• Single-Cell-Genomics-Group-CNAG-CRG / Tumor-Immune-Cell-Atlas
  Code repository for the Tumor Immune Cell Atlas (TICA) project
  ☆61Updated 3 years ago
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆90Updated 5 months ago
• pachterlab / voyager
  From geospatial to spatial -omics
  ☆93Updated 2 months ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆60Updated 2 years ago
• Coolgenome / iTALK
  ☆61Updated 5 years ago
• immunogenomics / SCENT
  Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
  ☆74Updated last month
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆86Updated 11 months ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆45Updated 11 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆70Updated 2 years ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆68Updated last month
• colomemaria / epiAneufinder
  R package to detect breakpoints and assign somies to scATAC-seq data
  ☆39Updated this week
• guokai8 / scGSVA
  scGSVA: Perform GSVA for single cell RNA seq
  ☆61Updated 6 months ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆41Updated last month
• elimereu / matchSCore2
  ☆55Updated 4 years 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
• data2intelligence / CytoSig
  ☆50Updated 8 months ago