Alternatives and similar repositories for SCARlink:

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

• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆66Updated last week
• Teichlab / Genes2Genes
  Aligning gene expression trajectories of single-cell reference and query systems
  ☆60Updated 5 months ago
• buenrostrolab / FigR
  Functional Inference of Gene Regulation
  ☆40Updated 8 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated last week
• rargelaguet / mouse_organogenesis_10x_multiome_publication
  Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""
  ☆40Updated 2 years ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆39Updated 2 months ago
• aerickso / SpatialInferCNV
  Clone Calling from Visium Spatial Transcriptomics of Cancer samples
  ☆62Updated 2 years ago
• BlishLab / scriabin
  Analysis of cell-cell communication at single-cell resolution
  ☆100Updated 6 months ago
• HYsxe / PRINT
  ☆36Updated 6 months ago
• Single-Cell-Genomics-Group-CNAG-CRG / TonsilAtlas
  Scripts and notebooks to reproduce all analysis from Massoni-Badosa et al. (2022)
  ☆28Updated 2 months ago
• immunogenomics / LISI
  Methods to compute Local Inverse Simpson's Index (LISI)
  ☆61Updated 3 years ago
• aet21 / SCENT
  Estimation of Single-Cell Potency with Single Cell Entropy
  ☆40Updated last year
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆52Updated 6 months ago
• caleblareau / mtscATACpaper_reproducibility
  Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020
  ☆16Updated last year
• kunwang34 / PhyloVelo
  PhyloVelo, Phylogeny-based transcriptomic velocity of single cells
  ☆43Updated last year
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆56Updated 11 months ago
• zhengrongbin / MEBOCOST
  A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
  ☆71Updated 4 months ago
• shyhihihi / MERCI
  MERCI for tracing of mitochondrion transfer between single cancer and T cells
  ☆21Updated 10 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆61Updated 6 months ago
• KlugerLab / DAseq
  ☆40Updated 3 years ago
• FloWuenne / scFunctions
  Functions for single cell data analysis
  ☆31Updated 3 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
• aertslab / create_cisTarget_databases
  Create cisTarget databases
  ☆46Updated last month
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 9 months ago
• theislab / regvelo
  inferring regulatory cellular dynamics
  ☆35Updated 2 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 10 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 weeks ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆58Updated 2 years ago
• harbourlab / uphyloplot2
  Draw phylogenetic trees of tumor evolution
  ☆75Updated last year
• beyondpie / CEMBA_wmb_snATAC
  Whole mouse brain snATAC seq analysis
  ☆24Updated 5 months ago