Alternatives and similar repositories for GEOparse

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

• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆132Updated 10 months ago
• sebriois / biomart
  Python biomart API
  ☆69Updated 2 years ago
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆238Updated 11 months ago
• r-bioinformatics / edgePy
  A Python implementation of edgeR for differential expression analysis
  ☆104Updated 6 years ago
• biothings / mygene.py
  mygene is an easy-to-use Python wrapper to access MyGene.Info services.
  ☆95Updated 11 months ago
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆67Updated 2 years ago
• jrderuiter / pybiomart
  A simple pythonic interface to biomart.
  ☆57Updated 5 years ago
• churchmanlab / genewalk
  GeneWalk identifies relevant gene functions for a biological context using network representation learning
  ☆133Updated last year
• antigenomics / vdjdb-db
  🗂️ [vdjdb.cdr3.net server will undergo maintenance this December, web site may be unreachable!] Git-based TCR database storage & managem…
  ☆149Updated 2 weeks ago
• kundajelab / bpnet
  Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
  ☆169Updated 2 months ago
• mikessh / vdjtools
  [Deprecated, see https://github.com/antigenomics/mirpy and other tools @antigenomics] Post-analysis of immune repertoire sequencing data
  ☆142Updated last year
• kundajelab / tfmodisco
  TF MOtif Discovery from Importance SCOres
  ☆161Updated 2 weeks ago
• openvax / gtfparse
  Parsing tools for GTF (gene transfer format) files
  ☆122Updated 10 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated this week
• openvax / mhctools
  Python interface to running command-line and web-based MHC binding predictors
  ☆99Updated last year
• GangCaoLab / CoolBox
  Jupyter notebook based genomic data visualization toolkit.
  ☆249Updated 3 weeks ago
• Xinglab / DARTS
  Deep-learning Augmented RNA-seq analysis of Transcript Splicing
  ☆115Updated last year
• scverse / muon
  muon is a multimodal omics Python framework
  ☆257Updated 2 weeks ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆243Updated 6 months ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆234Updated 2 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 3 years ago
• kipoi / models
  Model zoo for genomics
  ☆173Updated last week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆205Updated 2 months ago
• saezlab / pypath
  Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotat…
  ☆155Updated this week
• Illumina / PrimateAI
  deep residual neural network for classifying the pathogenicity of missense mutations.
  ☆115Updated 4 years ago
• kipoi / kipoi
  Kipoi's model zoo API
  ☆240Updated last week
• broadinstitute / depmap_omics
  What you need to process the Quarterly DepMap-Omics releases from Terra
  ☆125Updated 3 months ago
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆96Updated 5 years ago
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆149Updated last year
• Teichlab / bbknn
  Batch balanced KNN
  ☆176Updated 2 years ago