Alternatives and similar repositories for pySCTransform:

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

• 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
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆64Updated last month
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆28Updated 4 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
  ☆52Updated 7 months ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆61Updated 11 months ago
• lilab-bcb / harmony-pytorch
  ☆51Updated last week
• wallet-maker / cytopus
  Single cell omics biology annotations
  ☆51Updated last month
• lcmmichielsen / scHPL
  ☆35Updated last month
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated last week
• PMBio / MuDataSeurat
  .h5mu files interface for Seurat
  ☆29Updated last year
• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆53Updated 2 weeks ago
• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆41Updated last year
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆99Updated last year
• immunogenomics / cna
  Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…
  ☆48Updated this week
• HYsxe / PRINT
  ☆35Updated 7 months ago
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆66Updated this week
• rajewsky-lab / spacemake
  ☆42Updated this week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆27Updated last year
• earmingol / cell2cell
  User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
  ☆59Updated 10 months ago
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆22Updated 5 months ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆29Updated 3 weeks ago
• tgac-vumc / BLADE
  BLADE: Bayesian Log-normAl DEconvolution for enhanced in silico microdissection of bulk gene expression data
  ☆27Updated last year
• zakieh-tayyebi / CellSpace
  Scalable sequence-informed embedding of single-cell ATAC-seq data with CellSpace
  ☆40Updated 3 months ago
• MacoskoLab / slideseq-tools
  Tools for analyzing Slide-seq data
  ☆31Updated last year
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆31Updated last week
• Teichlab / sctk
  ☆36Updated 6 months ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆42Updated last year
• atarashansky / SCTransformPy
  A python port of the R package SCTransform:
  ☆19Updated 3 years ago
• raphael-group / STARCH
  Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
  ☆25Updated 8 months ago
• ratschlab / scim
  Code for Universal Single-Cell Matching with Unpaired Feature Sets
  ☆21Updated 3 years ago