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
  ☆689Updated last month
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆463Updated last year
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆593Updated last year
• reneshbedre / bioinfokit
  Bioinformatics data analysis and visualization toolkit
  ☆366Updated last year
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆862Updated last year
• tanghaibao / goatools
  Python library to handle Gene Ontology (GO) terms
  ☆876Updated last month
• mortazavilab / PyWGCNA
  PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
  ☆288Updated 11 months ago
• bionumpy / bionumpy
  Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
  ☆291Updated 7 months ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆413Updated this week
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆890Updated last week
• pachterlab / BI-BE-CS-183-2023
  Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
  ☆515Updated 3 weeks ago
• Illumina / SpliceAI
  A deep learning-based tool to identify splice variants
  ☆483Updated this week
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆451Updated last week
• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆773Updated last month
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆443Updated last month
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆493Updated last week
• deanslee / FigureOneLab
  Hone computational biology skills by re-enacting Figure 1 of modern biology papers
  ☆264Updated last year
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆486Updated last month
• calico / basenji
  Sequential regulatory activity predictions with deep convolutional neural networks.
  ☆462Updated 3 weeks ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆491Updated 8 months ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆397Updated 2 months ago
• evanpeikon / Bioinformatics_Toolkit
  A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessib…
  ☆461Updated last month
• theislab / single-cell-best-practices
  https://www.sc-best-practices.org
  ☆1,132Updated last week
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆573Updated 7 months ago
• openvax / pyensembl
  Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
  ☆399Updated 5 months ago
• mdozmorov / HiC_tools
  A collection of tools for Hi-C data analysis
  ☆630Updated last week
• pachterlab / gget
  🧬 gget enables efficient querying of genomic reference databases
  ☆1,094Updated this week
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆406Updated 4 months ago
• hbctraining / DGE_workshop
  ☆408Updated 4 years ago
• milaboratory / mixcr
  MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
  ☆381Updated this week