Alternatives and similar repositories for Cassiopeia

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

• rajewsky-lab / spacemake
  ☆48Updated last week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆31Updated 2 years ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 5 months ago
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆95Updated last year
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆66Updated 4 months ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated 7 months 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
  ☆56Updated last year
• HYsxe / PRINT
  ☆37Updated last year
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated 3 months ago
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆29Updated last week
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆123Updated last week
• nimwegenLab / cellstates
  Finding gene expression states in scRNA-seq data
  ☆51Updated last year
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆54Updated last year
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆43Updated last week
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆34Updated 8 months ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆109Updated 2 weeks ago
• welch-lab / MultiVelo
  Multi-omic velocity inference
  ☆113Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆128Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆56Updated 6 months 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
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• ebi-gene-expression-group / scanpy-scripts
  Scripts for using scanpy
  ☆38Updated last month
• AllonKleinLab / PBA
  Population balance analysis
  ☆44Updated 6 years ago
• calico / solo
  software to detect doublets
  ☆95Updated 11 months ago
• hmatsu1226 / SCODE
  SCODE : an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
  ☆45Updated 5 years ago
• lilab-bcb / harmony-pytorch
  ☆58Updated 6 months ago
• broadinstitute / epi-SHARE-seq-pipeline
  Epigenomics Program pipeline to analyze SHARE-seq data.
  ☆23Updated 8 months ago
• lcmmichielsen / scHPL
  ☆37Updated 9 months ago
• gifford-lab / prescient
  Codebase for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs) for generative modeling of single-cell time-series.
  ☆50Updated 10 months ago
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆51Updated this week