immunology

There are 11 repositories under immunology topic.

• milaboratory / mixcr

  MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

  10xantibodybioinformaticsimmunologyrep-seqrna-seqsequencingsingle-cellt-cellt-cell-receptor
  Language:Kotlin 311

• immunomind / immunarch

  🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

  immunologytcrtcr-repertoireimmunoinformaticsimmune-repertoirerep-seqbcr-repertoirebcrigig-repertoirebioinformaticsimmune-repertoire-dataimmune-repertoire-analysist-cell-receptorb-cell-receptorimmunoglobulinrepertoire-analysisairr-analysissingle-cellsingle-cell-analysis
  Language:R 290
• awesome-vdj

  slowkow / awesome-vdj

  📚 Tools and databases for analyzing HLA and VDJ genes.

  bioinformaticsimmunologyantibodyt-cell-receptorhla-databasehla-typingb-cell-receptorawesome-listhlabcrtcrvdj
  187

• whitews / FlowKit

  A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

  cytometryfcspythongatingmlflow-cytometryflow-cytometry-analysisfcs-filesflowjodata-scienceimmunology
  Language:Python 148

• antigenomics / vdjdb-db

  🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!

  bioinformaticsimmunologydatabaseantigent-cell
  Language:Groovy 127

• mikessh / vdjtools

  Post-analysis of immune repertoire sequencing data

  antibodybioinformaticsimmunologyrep-seqrepertoirestatt-cellt-cell-receptor
  Language:Groovy 126

• greenelab / covid19-review

  A collaborative review of the emerging COVID-19 literature. Join the chat here:

  covid-19sars-cov-2manuscriptmanubotreviewvirusimmunologyhacktoberfest
  Language:TeX 116

• sidhomj / DeepTCR

  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

  deep-learningrepertoiretcradaptive-immunityimmunologytcr-repertoire
  Language:Jupyter Notebook 109

• nf-core / hlatyping

  Precision HLA typing from next-generation sequencing data

  hlahla-typingimmunologydnarnaoptitypepersonalized-medicinenf-corenextflowworkflowpipeline
  Language:Nextflow 52

• mikessh / migmap

  HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

  antibodybioinformaticsimmunologyngsrep-seqsequencingt-cellt-cell-receptor
  Language:Groovy 50

• qmarcou / IGoR

  IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

  inferenceigorrecombinationimmunologysimulationhypermutation
  Language:C 49
• stitchr

  JamieHeather / stitchr

  Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

  tcrbioinformatics-toolimmunology
  Language:Python 48

• CRI-iAtlas / shiny-iatlas

  An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app

  genomicssystems-biologyimmunologycancer
  Language:R 47

• dmnfarrell / epitopepredict

  Python package and command line tool for epitope prediction

  epitope-prediction-methodsimmunologybioinformatics
  Language:Jupyter Notebook 46

• andrewrech / antigen.garnish

  peptidesbioinformaticsmachine-learningimmunologyimmunoinformatics
  Language:R 44

• mikessh / migec

  A RepSeq processing swiss-knife

  adapterantibodybioinformaticsimmunologyngsrep-seqsequencingumi
  Language:Groovy 41

• burtonrj / CytoPy

  A data-centric flow/mass cytometry automated analysis framework

  cytometry-analysis-pipelinecytometry-datacytometrypythonmongodbdocument-databaseflow-cytometryflow-cytometry-analysismass-cytometryimmunologyimmunophenotypingmachine-learningclusteringframework
  Language:Python 39

• whitews / FlowIO

  A Python library for reading and writing Flow Cytometry Standard (FCS) files

  pythonfcsflow-cytometryflow-cytometry-analysisflow-cytometry-filesfcs-filescytometryimmunology
  Language:Python 38

• Japrin / sscClust

  simpler single cell RNAseq data clustering

  bioinformaticsclusteringgenomicsimmunologysingle-cell
  Language:R 37

• imminfo / tcr

  [DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.

  immunoinformaticsimmunologytcrdata-analysisigtcr-repertoireig-repertoirebioinformaticsbioinformatics-analysis
  Language:R 36

• LCSB-BioCore / GigaSOM.jl

  Huge-scale, high-performance flow cytometry clustering in Julia

  somcytometrylarge-scalehuge-scaleclusteringself-organizing-mapartificial-intelligenceartifical-neural-networkflow-cytometryclustering-methodsneural-networksmass-cytometrycytofimmunology
  Language:Julia 29

• antigenomics / vdjviz

  ⚙️ A lightweight immune repertoire browser

  bioinformaticsbrowserimmunologyrep-seqweb
  Language:JavaScript 27

• BaderLab / HumanLiver

  R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

  rsingle-celldatasetliverimmunology
  Language:R 27

• PaccMann / TITAN

  Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2021)

  deep-learningimmunologytcr-epitopecompound-protein-interactionprotein-ligand
  Language:Jupyter Notebook 27

• RGLab / ImmuneSpaceR

  An R Interface to the ImmuneSpace database portal

  bioconductorlabkeyimmunespaceimmunologyhipcimmport
  Language:R 24

• uio-bmi / compairr

  Comparison of Adaptive Immune Receptor Repertoires

  immune-repertoireairrbioinformaticsimmunologyrepertoire-analysisimmunoinformaticsrep-seq
  Language:C++ 24

• burkesquires / immunology-informatics

  Immunology Informatics - Big Data Analysis in Immunology - Tutorials

  tutorialbioinformaticsimmunologyreproducible-researchflow-cytometryrna-seqcommand-lineanalysisdata-analysis
  Language:R 21

• rnabioco / djvdj

  An R package to analyze single-cell V(D)J data

  single-cell-rna-seqimmunoinformaticsimmunologyvdj
  Language:R 21

• arosenfeld / immunedb

  ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

  pythonbioinformaticsimmunologydatabase
  Language:Python 19
• hifihla

  PacificBiosciences / hifihla

  An HLA star-calling tool for PacBio HiFi data types

  dnahifihlahla-typingimgtimmunologypacbiosequencing
  18
• hlabud

  slowkow / hlabud

  🐶 hlabud: HLA genotype analysis in R

  bioinformaticshlageneticsimmunoinformaticsimmunologyhla-database
  Language:TeX 14

• lkuchenb / MultiHLA

  WES HLA Typing based on multiple alternative tools

  workflowimmunologyimmunoinformaticssequencingexomegenome
  Language:Python 13

• ShawHahnLab / vquest

  Automate IMGT V-QUEST usage on imgt.org

  bioinformaticsimmunologyimgt
  Language:Python 12

• MarioniLab / ImmuneAging2017

  Code for Celia and Nils' immune aging project.

  single-cellimmunologyaging
  Language:R 10
• AIMS

  ctboughter / AIMS

  AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below site for documentation

  bioinformaticsimmunologybiophysicspython3kivy
  Language:Jupyter Notebook 9

• immunomind / 2019-airr-genova-tutorial-pytorch

  Incredible Deep Learning in immunooncology with Pytorch - workshop at AIRR Community Meeting IV

  immunologypytorchpytorch-tutorialmhcimmunoinformatics
  Language:Jupyter Notebook 9