Alternatives and similar repositories for scim:

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

• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆48Updated 2 weeks 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 2 years ago
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆38Updated 2 months ago
• CostaLab / scopen
  scOpen: single-cell open chromatin analysis via NMF modelling
  ☆26Updated 2 years ago
• GreenleafLab / brainchromatin
  Code used to analyze single cell RNA and ATAC sequencing in developing human brain
  ☆33Updated 3 years ago
• forrest-lab / NATMI
  NATMI: Network Analysis Toolkit for the Multicellular Interactions
  ☆34Updated 3 years ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated last year
• jcao89757 / TESSA
  Mapping the Functional Landscape of TCR Repertoire
  ☆34Updated 3 years ago
• lcmmichielsen / scHPL
  ☆35Updated 2 weeks ago
• zhanglhbioinfor / DIRECT-NET
  ☆10Updated last year
• wanglab-broad / CAST
  CAST package
  ☆31Updated 4 months ago
• jingshuw / SAVERX
  R package for transfer learning of single-cell RNA-seq denoising
  ☆29Updated 2 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 10 months ago
• doraadong / TraSig
  Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data
  ☆24Updated 2 years ago
• hsmaan / Iniquitate
  Analysis of imbalanced data and its impacts in a scRNA-seq integration setting
  ☆30Updated last week
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆26Updated 3 months ago
• raphael-group / CalicoST
  Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
  ☆33Updated last week
• whhudson / spatialTCR
  ☆12Updated 3 years ago
• KChen-lab / bindSC
  Bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and…
  ☆34Updated last year
• jbergenstrahle / STUtility
  ☆47Updated 2 years ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆28Updated 3 months ago
• AllonKleinLab / cospar
  ☆26Updated last year
• caleblareau / maegatk
  Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
  ☆19Updated last year
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated 3 months ago
• caokai1073 / UnionCom
  The Software of UnionCom Algorithm
  ☆25Updated 7 months ago
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• liulab-dfci / lisa2
  ☆30Updated 2 years ago
• PeterZZQ / CellPath
  ☆20Updated 2 years ago
• LungCellAtlas / scRNAseq_pipelines
  Repository for the building, sharing and editing of scRNAseq pipelines for the Lung Cell Atlas
  ☆33Updated 4 years ago