Alternatives and similar repositories for SCTransformPy:

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

• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 9 months ago
• lilab-bcb / harmony-pytorch
  ☆51Updated this week
• theislab / spatial_scog_workshop_2022
  Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
  ☆53Updated 2 years ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆41Updated last month
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆50Updated last week
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 10 months ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆63Updated last month
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆54Updated last week
• dpeerlab / ENVI
  ☆45Updated this week
• StatBiomed / SpatialDM
  Spatial direct messaging detected by bivariate Moran
  ☆25Updated 2 months ago
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆71Updated 2 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 2 years ago
• zcang / SpaOTsc
  ☆45Updated 2 years ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆60Updated 2 months ago
• YosefLab / popV
  ☆71Updated last week
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆102Updated last year
• snehamitra / SCARlink
  ☆50Updated 6 months ago
• yunguan-wang / SPROD
  SPROD: Spatial expression profiling de-noising
  ☆36Updated last year
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆66Updated last year
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆45Updated 8 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆29Updated this week
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆61Updated 6 months ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆56Updated 11 months ago
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆59Updated 10 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆66Updated last week
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆110Updated 2 weeks ago
• data2intelligence / SpaCET
  Spatial Cellular Estimator for Tumors
  ☆50Updated 2 weeks ago
• SchubertLab / mvTCR
  ☆51Updated 4 months ago
• multitalk / awesome-cell-cell-communication
  Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics
  ☆39Updated 2 weeks ago