immunoinformatics

There are 3 repositories under immunoinformatics topic.

immunomind / immunarch
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
immunology tcr tcr-repertoire immunoinformatics immune-repertoire rep-seq bcr-repertoire bcr ig ig-repertoire bioinformatics immune-repertoire-data immune-repertoire-analysis t-cell-receptor b-cell-receptor immunoglobulin repertoire-analysis airr-analysis single-cell single-cell-analysis
Language:R 290
jostmey / MaxSnippetModel
Statistical classifier for immune repertoires
immune-repertoires immunoinformatics machine-learning multiple-sclerosis statistics tensorflow
Language:Python 45
svalkiers / clusTCR
CDR3 clustering module providing a new method for fast and accurate clustering of large data sets of CDR3 amino acid sequences, and offering functionalities for downstream analysis of clustering results.
faiss immunoinformatics markov-clustering-algorithm
Language:Python 44
andrewrech / antigen.garnish
peptides bioinformatics machine-learning immunology immunoinformatics
Language:R 42
immunomind / covid19
🦠 Regularly updated list of publicly available datasets with single-cell (scRNAseq) and T-cell/antibody immune repertoire (AIRR / RepSeq / immunosequencing) data of COVID-19 patients with SARS-CoV-2.
covid-19 covid-19-data sars-cov-2 t-cell antibody rep-seq immune-repertoire-data single-cell-data scrna-seq-data airr-analysis bioinformatics immunoinformatics computational-immunology
42
imminfo / tcr
[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.
immunoinformatics immunology tcr data-analysis ig tcr-repertoire ig-repertoire bioinformatics bioinformatics-analysis
Language:R 36
uio-bmi / compairr
Comparison of Adaptive Immune Receptor Repertoires
airr bioinformatics immune-repertoire immunoinformatics immunology rep-seq repertoire-analysis
Language:C++ 24
wuaipinglab / ImmuCC
Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
immunoinformatics deconvolution signature-genes gene-expression
Language:R 22
rnabioco / djvdj
An R package to analyze single-cell V(D)J data
single-cell-rna-seq immunoinformatics immunology vdj
Language:R 21
leonjessen / PepTools
PepTools - An Immunoinformatics (Immunological Bioinformatics) R-package for working with peptide data
research immunoinformatics bioinformatics datascience rstats r peptides peptide-data epitope-prediction-methods vaccine immunological-bioinformatics encoding-peptides
Language:R 16
setriq
BenTenmann / setriq
Fast string distance computation in Python
python cpp bioinformatics immunoinformatics
Language:Python 15
hlabud
slowkow / hlabud
🐶 hlabud: HLA genotype analysis in R
bioinformatics genetics hla hla-database immunoinformatics immunology
Language:TeX 14
lkuchenb / MultiHLA
WES HLA Typing based on multiple alternative tools
exome genome immunoinformatics immunology sequencing workflow
Language:Python 13
immunomind / 2019-airr-genova-tutorial-pytorch
Incredible Deep Learning in immunooncology with Pytorch - workshop at AIRR Community Meeting IV
immunology pytorch pytorch-tutorial mhc immunoinformatics
Language:Jupyter Notebook 9
IgGeneUsage
snaketron / IgGeneUsage
Comparison of gene usage in immune repertoires under different biological conditions
immune-repertoires differential-gene-expression high-throughput-sequencing immunoinformatics immunological-bioinformatics vdj-recombination differential-analysis tcr-repertoire bcr-repertoire b-cell-receptor immunology immunoglobulin immunogenomics immune-repertoire immune-repertoire-analysis
Language:R 6
ikmb / iptoolkit
A pythonic library for analysing immunopeptidomic experiments
seaborn hla immunoinformatics immunopeptidomics bioinformatics multiomics plotly data-science
Language:Python 4
MuteJester / LZGraphs
LZ76 Graphs and Applications in Immunology
genetics graph-theory immunoinformatics immunology markov-chain pgen
Language:Python 4
yutanagano / tidytcells
Standardise TR/MH data
bioinformatics data-cleaning immunoinformatics immunology standardization t-cell-receptor major-histocompatibility-complex mh mhc tcr tr bioinformatics-tool
Language:Python 4
dyohanne / RepAn
Analysis functions for deep sequenced immune repertoire (Repseq) datasets in R
immunoinformatics differential-abundance-analyses tcr-repertoire tcr tcrb bioinformatics bioinformatics-pipeline repseq
Language:R 3
imminfo / mhc
bioinformatics deep-learning immunoinformatics immunology machine-learning mhc
Language:Jupyter Notebook 3
immunomind / slides
Slides for presentations by ImmunoMind team
presentation-slides immunology bioinformatics immunoinformatics tcr-repertoire bcr-repertoire machine-learning deep-learning
3
mariomarroquim / eplogic
Scripts for Anti-HLA antibody target prediction via machine learning
cross-validation hla-eplets hla-matching imbalanced-data immunoinformatics immunology machine-learning scikit-learn single-antigen-beads
Language:HTML 3
mattfemia / iedb-python
Python SDK for Immune Epitope Database (IEDB) Analysis Tools API
t-cell tcr immunoinformatics immunology
Language:Python 3
mnielLab / NetTCR-2.2
Sequence-based prediction of peptide-TCR interactions using paired chain data
bioinformatics epitopes immunoinformatics immunology machine-learning t-cell-receptor
Language:Python 3
raghavagps / algpred2
A machine learning based method for predicting, scanning and mapping allergenic regions in an allergen
allergens allergy bioinformatics immunoinformatics immunotherapy machine-learning-algorithms
Language:Perl 3
esohkevin / NTD-MANE
Vaccine/Diagnostics Development Pipelines
bioinformatics immunoinformatics neglected-tropical-disease proteomics reverse-vaccinology vaccine-design
Language:Shell 2
eNERVE
francescopatane96 / eNERVE
eNERVE is a dynamic, high-throughput and standalone in silico reverse vaccinology pipeline for eukaryotic protein candidate vaccines (PVCs) discovery from entire proteomes (FASTA file).
bioinformatics bioinformatics-pipeline immunoinformatics immunology machine-learning reverse-vaccinology antigen-discovery vaccinology biotechnology pharmaceuticals research vaccines pipeline
Language:Jupyter Notebook 2
mariomarroquim / hla-antibody-analyzer
Electron app for performing HLA antibody analysis of reactivity panels
bootstrap4 css3 electronjs hla-matching html5 immunoinformatics immunology nodejs single-antigen-beads
Language:HTML 2
raghavagps / clbtope
An ensemble method for predicting linear and conformational B-cell epitope
b-cell-epitope-prediction bioinformatics immunoinformatics machine-learning-algorithms conformational-epitope
Language:Python 2
raghavagps / ifnepitope2
Prediction of interferon-gamma inducing peptides using alignment-based and alignment-free methods
bioinformatics immunoinformatics immunotherapy machine-learning-algorithms vaccine interferon-gamma
Language:Python 2
raghavagps / il13pred
A method for predicting cytokine IL-13 inducing peptides
bioinformatics immunoinformatics machine-learning-algorithms predictive-modeling vaccine
Language:Python 2
raghavagps / il5pred
Machine learning based method for predicting and scanning IL-5 inducing petides
bioinformatics immunoinformatics immunotherapeutics prediction-model inducing-peptides interleukin-5
Language:Python 2
raghavagps / il6pred
In silico model for predicting of Interleukin-6 inducing peptides
covid19 deeo-learning immunoinformatics machine-learning vaccine interleukin-6
Language:Python 2
snaketron / ClustIRR
Clustering of immune receptor repertoires
b-cell-receptor clustering quantitative-methods repertoire-analysis t-cell-receptor bioinformatics immunoinformatics immunology rep-seq
Language:R 2
meyer-lab-cshl / BATMAN
Bayesian inference of Activation of TCR by Mutant Antigens
bayesian-inference epitope-datasets epitope-immunogenicity-prediction epitope-prediction-methods immunoinformatics peptide-bioinformatics t-cell-response tcr-epitope
Language:Jupyter Notebook 1
raghavagps / hladr4pred2
An improved method for predicting binders of HLA-DRB1-04:01
blast-search immunoinformatics immunotherapeutics machine-learning-algorithms computer-aided-vaccine
Language:Python 1