Alternatives and similar repositories for pypath:

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

• saezlab / decoupler-py
  Python package to perform enrichment analysis from omics data.
  ☆184Updated last month
• saezlab / dorothea
  R package to access DoRothEA's regulons
  ☆143Updated last year
• broadinstitute / depmap_omics
  What you need to process the Quarterly DepMap-Omics releases from Terra
  ☆114Updated this week
• churchmanlab / genewalk
  GeneWalk identifies relevant gene functions for a biological context using network representation learning
  ☆130Updated 7 months ago
• Teichlab / bbknn
  Batch balanced KNN
  ☆154Updated last year
• LewisLabUCSD / Ligand-Receptor-Pairs
  Compendium of available lists of ligand-receptor pairs and surface-secreted protein interactions.
  ☆129Updated 2 years ago
• slowkow / awesome-vdj
  📚 Tools and databases for analyzing HLA and VDJ genes.
  ☆219Updated 3 months ago
• scverse / muon
  muon is a multimodal omics Python framework
  ☆230Updated 3 weeks ago
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆151Updated 2 years ago
• theislab / scarches
  Reference mapping for single-cell genomics
  ☆358Updated last month
• colomemaria / epiScanpy
  Episcanpy: Epigenomics Single Cell Analysis in Python
  ☆142Updated 3 months ago
• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆118Updated 2 years ago
• openvax / mhctools
  Python interface to running command-line and web-based MHC binding predictors
  ☆95Updated 5 months ago
• immunoengineer / gliph
  Grouping of Lymphocyte Interactions by Paratope Hotspots
  ☆91Updated 4 years ago
• wckdouglas / diffexpr
  Porting DESeq2 into python via rpy2
  ☆68Updated last year
• uio-bmi / immuneML
  immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
  ☆67Updated this week
• biothings / mygene.py
  mygene is an easy-to-use Python wrapper to access MyGene.Info services.
  ☆87Updated 2 months ago
• baryshnikova-lab / safepy
  Python implementation of Spatial Analysis of Functional Enrichment (SAFE)
  ☆41Updated this week
• antigenomics / vdjdb-db
  🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
  ☆135Updated 2 weeks ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆227Updated this week
• KrishnaswamyLab / SingleCellWorkshop
  ☆90Updated 4 years ago
• crazyhottommy / TCR-BCR-seq-analysis
  T/B cell receptor sequencing analysis notes
  ☆245Updated 3 months ago
• vahuynh / GENIE3
  Machine learning-based approach for the inference of gene regulatory networks from expression data.
  ☆78Updated 3 years ago
• phbradley / tcr-dist
  Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)
  ☆81Updated 3 years ago
• mousepixels / sanbomics
  bioinformatics plotting and tools
  ☆56Updated 9 months ago
• asncd / MIMOSCA
  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.
  ☆87Updated 5 years ago
• pinellolab / scATAC-benchmarking
  Benchmarking computational single cell ATAC-seq methods
  ☆182Updated 4 years ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆112Updated this week
• fraenkel-lab / OmicsIntegrator2
  Prize-Collecting Steiner Forests for Interactomes
  ☆59Updated 9 months ago
• FunctionLab / ExPecto
  predicting expression effects of human genome variants ab initio from sequence
  ☆127Updated last month