Alternatives and similar repositories for PyDESeq2:

Users that are interested in PyDESeq2 are comparing it to the libraries listed below

• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆622Updated 2 weeks ago
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆885Updated this week
• mortazavilab / PyWGCNA
  PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
  ☆242Updated 2 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆397Updated 4 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆458Updated 4 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆799Updated 9 months ago
• reneshbedre / bioinfokit
  Bioinformatics data analysis and visualization toolkit
  ☆349Updated 10 months ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆572Updated 8 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,015Updated last week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆691Updated last month
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆468Updated last month
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆360Updated last month
• hbctraining / DGE_workshop
  ☆389Updated 3 years ago
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆355Updated 3 weeks ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆326Updated 2 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆483Updated 4 years ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆411Updated 9 months ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆482Updated 2 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆338Updated 8 months ago
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆496Updated last year
• bionumpy / bionumpy
  Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
  ☆280Updated this week
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆302Updated 2 years ago
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆773Updated this week
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆603Updated this week
• cellgeni / sceasy
  A package to help convert different single-cell data formats to each other
  ☆418Updated last year
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆386Updated 4 months ago
• evanpeikon / Bioinformatics_Toolkit
  A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessib…
  ☆212Updated this week
• scverse / scanpy-tutorials
  Scanpy Tutorials.
  ☆213Updated last week
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆346Updated 3 months ago
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆434Updated last month