YosefLab / PopV

Related projects ⓘ

Alternatives and complementary repositories for PopV

• 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
• dpeerlab / ENVI
  ☆37Updated 3 weeks ago
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆48Updated last month
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆60Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆56Updated 4 months ago
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated last month
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆59Updated 6 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆36Updated 2 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆56Updated 3 months ago
• Moldia / Xenium_benchmarking
  Code used to benchmark Xenium
  ☆40Updated 4 months ago
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆28Updated 6 months ago
• whhudson / spatialTCR
  ☆12Updated 2 years ago
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆24Updated 6 months ago
• yunguan-wang / SPROD
  SPROD: Spatial expression profiling de-noising
  ☆33Updated last year
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆48Updated 7 months ago
• prabhakarlab / Banksy
  BANKSY: spatial clustering
  ☆73Updated 3 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆38Updated 3 years ago
• Teichlab / bin2cell
  Join subcellular Visium HD bins into cells
  ☆52Updated this week
• yelabucsf / scrna-parameter-estimation
  Direct estimation of mean and covariance from single cell RNA seq experiments
  ☆66Updated 5 months ago
• scverse / anndataR
  AnnData interoperability in R
  ☆58Updated this week
• xiaoyeye / TFvelo
  ☆40Updated 6 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆58Updated this week
• msraredon / NICHES
  Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
  ☆50Updated last month
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆85Updated last week
• Nanostring-Biostats / CosMx-Analysis-Scratch-Space
  This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained her…
  ☆32Updated this week
• zhengli09 / BASS
  Bayesian Analytics for Spatial Segmentation
  ☆21Updated last month
• HYsxe / PRINT
  ☆32Updated 2 months ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆61Updated 6 months ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆24Updated 3 weeks ago
• KlugerLab / DAseq
  ☆39Updated 3 years ago