Alternatives and similar repositories for PyWGCNA

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

• dylkot / cNMF
  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
  ☆342Updated 3 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆358Updated 4 months ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆369Updated 3 weeks ago
• NBISweden / workshop-scRNAseq
  Single cell RNA sequencing analysis course
  ☆214Updated last month
• STOmics / Stereopy
  A toolkit of spatial transcriptomic analysis.
  ☆245Updated last week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆356Updated 4 months ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆197Updated 3 months ago
• crazyhottommy / awesome_spatial_omics
  tools and notes for spatial omics
  ☆298Updated 3 months ago
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆196Updated this week
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆467Updated 2 weeks ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆236Updated 3 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆365Updated 2 weeks ago
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆213Updated last week
• broadinstitute / ssGSEA2.0
  Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
  ☆287Updated 3 weeks ago
• liulab-dfci / MAESTRO
  Single-cell Transcriptome and Regulome Analysis Pipeline
  ☆283Updated 2 years ago
• cellgeni / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆136Updated 2 years ago
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆632Updated this week
• CebolaLab / RNA-seq
  Step-by-step analysis pipeline for RNA-seq data
  ☆119Updated last year
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆425Updated last year
• broadinstitute / CellBender
  CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
  ☆331Updated 10 months ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆310Updated this week
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆280Updated 10 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆309Updated 4 years ago
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆260Updated last week
• digitalcytometry / ecotyper
  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
  ☆201Updated last year
• r3fang / SnapATAC
  Analysis Pipeline for Single Cell ATAC-seq
  ☆318Updated 2 years ago
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆215Updated 4 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated this week
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆396Updated this week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆541Updated last week