Alternatives and similar repositories for pySCTransform

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

• LouisFaure / scFates
  a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
  ☆65Updated last week
• potulabe / symphonypy
  Port of symphony algorithm of single-cell reference atlas mapping to Python
  ☆34Updated last month
• lilab-bcb / harmony-pytorch
  ☆62Updated 8 months ago
• rajewsky-lab / spacemake
  ☆49Updated last week
• pinellolab / pychromVAR
  A python package for chromVAR
  ☆33Updated 2 years ago
• emdann / milopy
  Python implementation of Milo for differential abundance testing on KNN graph
  ☆81Updated 11 months ago
• JCVenterInstitute / NSForest
  A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…
  ☆66Updated 5 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
  ☆57Updated last year
• bendemeo / shannonca
  Information-based dimensionality reduction
  ☆29Updated last year
• HYsxe / PRINT
  ☆37Updated 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 3 years ago
• jzhoulab / quasildr
  Quasilinear data representations for single-cell omics data analysis
  ☆43Updated 2 years ago
• bioFAM / mofapy2
  Multi-omics factor analysis v2
  ☆56Updated last week
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆79Updated this week
• ratschlab / scim
  Code for Universal Single-Cell Matching with Unpaired Feature Sets
  ☆22Updated 4 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆126Updated 2 months ago
• bioFAM / mofax
  Work with trained factor models in Python
  ☆36Updated last year
• saezlab / greta
  Benchmark of GRNs using the GRETA pipeline
  ☆31Updated this week
• YosefLab / mrvi_archive
  Multi-resolution Variational Inference
  ☆22Updated 2 weeks ago
• const-ae / pyLemur
  A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.
  ☆27Updated last year
• lcmmichielsen / scHPL
  ☆37Updated 2 weeks ago
• SCCAF / sccaf
  Single-Cell Clustering Assessment Framework
  ☆107Updated 2 years ago
• noamteyssier / adpbulk
  pseudobulking on an AnnData object
  ☆34Updated 10 months ago
• settylab / Mellon
  Non-parametric density inference for single-cell analysis.
  ☆73Updated 8 months ago
• Teichlab / sctk
  ☆45Updated last week
• Teichlab / snp2cell
  cell type specific, trait-associated gene regulation
  ☆29Updated 10 months ago
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆30Updated 3 weeks ago
• immunitastx / monkeybread
  Analyzing cellular niches in spatial transcriptomics data
  ☆34Updated last year
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆32Updated 3 months ago
• simonwm / tacco
  TACCO: Transfer of Annotations to Cells and their COmbinations
  ☆62Updated 5 months ago