Alternatives and similar repositories for scim

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

• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated 2 years ago
• GreenleafLab / brainchromatin
  Code used to analyze single cell RNA and ATAC sequencing in developing human brain
  ☆33Updated 3 years ago
• 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 3 years ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆64Updated 2 weeks ago
• AllonKleinLab / cospar
  ☆26Updated last year
• PeterZZQ / CellPath
  ☆21Updated 3 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆64Updated 2 months ago
• wanglab-broad / CAST
  CAST package
  ☆40Updated 10 months ago
• CostaLab / scMEGA
  scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
  ☆40Updated 11 months ago
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 9 months ago
• kharchenkolab / scITD
  Single-Cell Analysis of Inter-Individual Variability by Interpretable Tensor Decomposition
  ☆61Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆55Updated 3 months ago
• KChen-lab / bindSC
  Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…
  ☆36Updated 2 years ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆28Updated last week
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆105Updated last year
• mvinyard / ArchR-h5ad
  Parse ArchR arrow files to anndata h5ad
  ☆15Updated last year
• theislab / cross_system_integration
  ☆13Updated 2 weeks ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆41Updated last month
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆25Updated 2 years ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆35Updated 4 years ago
• theMILOlab / SPATA
  SPATA Package for spatial gene expression analysis
  ☆21Updated 3 years ago
• klarman-cell-observatory / hdst
  ☆19Updated 6 years ago
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆60Updated last month
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 months ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆41Updated 8 months ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆29Updated last week
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆65Updated 3 weeks ago
• JEFworks-Lab / veloviz
  RNA-velocity informed embeddings for visualizing cellular trajectories
  ☆45Updated 3 years ago
• jbergenstrahle / STUtility
  ☆53Updated 2 years ago
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆34Updated 3 years ago