Alternatives and similar repositories for SCTransformPy:

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

• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆68Updated 2 months ago
• lilab-bcb / harmony-pytorch
  ☆53Updated last month
• YosefLab / scib-metrics
  Accelerated, Python-only, single-cell integration benchmarking metrics
  ☆58Updated last week
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated last year
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated 2 weeks ago
• Teichlab / cellhint
  A tool for semi-automatic cell type harmonization and integration
  ☆104Updated last month
• YosefLab / popV
  ☆73Updated last week
• Teichlab / drug2cell
  Gene group activity utility functions for Scanpy
  ☆74Updated 4 months ago
• 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
• GuangyuWangLab2021 / cellDancer
  Predict RNA velocity through deep learning
  ☆69Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆60Updated 10 months ago
• mossjacob / pyslingshot
  Python implementation of the Slingshot pseudotime algorithm
  ☆60Updated last year
• 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
• snehamitra / SCARlink
  ☆50Updated 7 months ago
• BayraktarLab / cell2fate
  Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.
  ☆73Updated last month
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆68Updated last month
• shuxiaoc / maxfuse
  ☆51Updated 11 months ago
• dpeerlab / ENVI
  ☆48Updated last month
• whhudson / spatialTCR
  ☆13Updated 3 years ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆68Updated 3 weeks ago
• raphael-group / GASTON
  GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
  ☆49Updated 3 months ago
• drieslab / awesome-spatial-data-analysis
  Awesome list of tools and methods to perform spatial transcriptomic data analysis.
  ☆40Updated 3 years ago
• yunguan-wang / SPROD
  SPROD: Spatial expression profiling de-noising
  ☆36Updated last year
• CSOgroup / cellcharter
  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
  ☆119Updated last week
• seqscope / ficture
  ☆34Updated 2 weeks ago
• saketkc / pySCTransform
  Python package to perform normalization and variance-stabilization of single-cell data
  ☆23Updated 3 weeks ago
• raphael-group / paste2
  Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
  ☆34Updated 2 months ago
• icbi-lab / luca
  Single-cell Lung Cancer Atlas with 1.2M cells
  ☆62Updated 3 months ago
• SchubertLab / mvTCR
  ☆51Updated 6 months ago
• KlugerLab / GeneTrajectory
  R implementation of GeneTrajectory
  ☆58Updated last year