Alternatives and similar repositories for PyWGCNA

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

• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆387Updated 3 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆239Updated 4 months ago
• scverse / decoupler
  Python package to perform enrichment analysis from omics data.
  ☆212Updated last week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆199Updated 4 months ago
• scverse / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆268Updated last week
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆234Updated last week
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆257Updated 3 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆366Updated 6 months ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆228Updated 2 months ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆218Updated this week
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆316Updated last week
• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆347Updated 4 months ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆259Updated 7 months ago
• Winnie09 / GPTCelltype
  ☆206Updated last year
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆366Updated 6 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆375Updated last month
• zhangyuqing / ComBat-seq
  Batch effect adjustment based on negative binomial regression for RNA sequencing count data
  ☆182Updated 4 years ago
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆141Updated 2 years ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆219Updated 3 months ago
• cortes-ciriano-lab / SComatic
  A tool for detecting somatic variants in single cell data
  ☆208Updated 10 months ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆643Updated last month
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆234Updated 3 weeks ago
• aertslab / scenicplus
  SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…
  ☆229Updated 5 months ago
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆289Updated 3 weeks ago
• mdozmorov / HiC_data
  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
  ☆191Updated 3 weeks ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆233Updated 6 months ago
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆204Updated last year
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆184Updated 4 years ago
• Cloufield / gwaslab
  A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
  ☆224Updated last week
• IanevskiAleksandr / sc-type
  ☆269Updated 8 months ago