Alternatives and similar repositories for Cassiopeia

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

• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated last year
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆82Updated 7 months ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆49Updated 10 months ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆30Updated 2 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated last year
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆32Updated 2 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆68Updated 3 months 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
• 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
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆52Updated 9 months ago
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆28Updated 2 years ago
• calico / solo
  software to detect doublets
  ☆92Updated 5 months ago
• lilab-bcb / harmony-pytorch
  ☆54Updated last week
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆24Updated 2 weeks ago
• HYsxe / PRINT
  ☆35Updated 8 months ago
• rajewsky-lab / spacemake
  ☆44Updated last week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆74Updated 2 months ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated last month
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆134Updated last week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆117Updated 9 months ago
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 11 months ago
• tanaylab / metacells
  Metacells - Single-cell RNA Sequencing Analysis
  ☆107Updated 8 months ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆75Updated last month
• theislab / scib-pipeline
  Snakemake pipeline that works with the scIB package to benchmark data integration methods.
  ☆73Updated 4 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated last month
• cole-trapnell-lab / cicero-release
  ☆59Updated 9 months ago
• lcmmichielsen / scHPL
  ☆35Updated 2 months ago
• nimwegenLab / cellstates
  Finding gene expression states in scRNA-seq data
  ☆51Updated last year
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆38Updated last week
• scverse / mudata
  Multimodal Data (.h5mu) implementation for Python
  ☆98Updated last week