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
  ☆70Updated 6 months ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆106Updated last month
• GfellerLab / SuperCell
  Coarse-graining of large single-cell RNA-seq data into metacells
  ☆73Updated 6 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆71Updated 10 months ago
• omnideconv / omnideconv
  Unified access to several second-generation deconvolution methods
  ☆65Updated 3 weeks ago
• carmonalab / STACAS
  R package for semi-supervised single-cell data integration
  ☆79Updated last year
• immunogenomics / SCENT
  Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA
  ☆72Updated 6 months ago
• swaruplabUCI / ArchRtoSignac
  An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  ☆35Updated 6 months ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆57Updated 2 years ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆61Updated 2 years ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆40Updated last week
• stemangiola / CuratedAtlasQueryR
  Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
  ☆90Updated 2 months ago
• Coolgenome / iTALK
  ☆59Updated 5 years ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆56Updated 2 years ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆40Updated 8 months ago
• KChen-lab / METAFlux
  ☆61Updated 8 months ago
• MarioniLab / miloDE
  Framework for sensitive DE testing (using neighbourhoods)
  ☆64Updated 7 months ago
• AntonioDeFalco / SCEVAN
  R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the …
  ☆98Updated 3 weeks ago
• colomemaria / epiAneufinder
  R package to detect breakpoints and assign somies to scATAC-seq data
  ☆34Updated last week
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆31Updated 9 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆59Updated 6 months ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 6 months ago
• arc85 / celltalker
  Inference of cell-cell communication from single-cell RNAseq data
  ☆48Updated last year
• elimereu / matchSCore2
  ☆53Updated 4 years ago
• ncborcherding / utility
  Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR
  ☆84Updated 8 months ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆59Updated last month
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆60Updated 4 months ago
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆56Updated this week
• RausellLab / CelliD
  Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.
  ☆93Updated last year
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆72Updated 4 years ago