Alternatives and similar repositories for GEOparse:

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

• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆224Updated 3 weeks ago
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆196Updated last year
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆68Updated last year
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆226Updated this week
• r-bioinformatics / edgePy
  A Python implementation of edgeR for differential expression analysis
  ☆99Updated 5 years ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆146Updated 2 years ago
• brianhie / scanorama
  Panoramic stitching of single cell data
  ☆271Updated 10 months ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆141Updated 2 months ago
• antigenomics / vdjdb-db
  🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
  ☆133Updated this week
• mikessh / vdjtools
  [REPLACED by https://github.com/antigenomics/mirpy] Post-analysis of immune repertoire sequencing data
  ☆134Updated 8 months ago
• liulab-dfci / TRUST4
  TCR and BCR assembly from RNA-seq data
  ☆293Updated this week
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆125Updated 2 weeks ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆278Updated 7 months ago
• openvax / pyensembl
  Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
  ☆388Updated 8 months ago
• ANHIG / IMGTHLA
  Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute
  ☆218Updated this week
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆213Updated 2 weeks ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆357Updated 2 weeks ago
• linnarsson-lab / loompy
  Python implementation of the Loom file format - http://loompy.org
  ☆142Updated 2 months ago
• czbiohub-sf / tabula-muris
  Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
  ☆190Updated last year
• Teichlab / SpatialDE
  Test genes for Spatial Variation
  ☆157Updated 9 months ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆180Updated 4 years ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆123Updated 4 years ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆331Updated last month
• dviraran / xCell
  Cell types enrichment analysis
  ☆191Updated 8 months ago
• kaizhang / SnapATAC2
  Single-cell epigenomics analysis tools
  ☆247Updated last month
• scverse / muon
  muon is a multimodal omics Python framework
  ☆225Updated 2 weeks ago
• velocyto-team / velocyto.py
  RNA velocity estimation in Python
  ☆164Updated last year
• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆179Updated last week
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆108Updated 3 months ago
• tabdelaal / scRNAseq_Benchmark
  Bench-marking classification tools for scRNA-seq data
  ☆183Updated 2 years ago