AntigenOmics
Mining antigen and antigen receptor repertoires. Immune repertoire biomarker databases and software tools.
Russian Federation
Pinned Repositories
repseq-annotation-tutorial
📝 [Tutorial] RepSeq data mining basics in R
repseq-protocol-comparison
📝 [Paper] Comparative analysis of immune repertoire profiling protocols
tcr-annotation-methodology
📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery
tcren-ms
📝 [Paper] TCRen: predicting TCR-peptide recognition based on residue-level pairwise statistical potential
vdjdb-classifier-benchmark
vdjdb-db
🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
vdjdb-motifs
⚙️ Motif inference for the VDJdb database
vdjdb-web
Interactive browser for the VDJdb database
vdjmatch
⚙️ Matching T-cell repertoire against a database of TCR antigen specificities
vdjviz
⚙️ A lightweight immune repertoire browser
AntigenOmics's Repositories
antigenomics/vdjdb-db
🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
antigenomics/vdjviz
⚙️ A lightweight immune repertoire browser
antigenomics/tcren-ms
📝 [Paper] TCRen: predicting TCR-peptide recognition based on residue-level pairwise statistical potential
antigenomics/vdjdb-web
Interactive browser for the VDJdb database
antigenomics/tcr-annotation-methodology
📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery
antigenomics/ipred
Antigen immunogenicity prediction
antigenomics/vdjdb-classifier-benchmark
antigenomics/vdjdb-motifs
⚙️ Motif inference for the VDJdb database
antigenomics/vdjsight
[under development] Next-generation immunome browser
antigenomics/covid19-tcr-analysis
Identification and analysis of TCR motifs specific to SARS-CoV-2 epitopes
antigenomics/trab-pairing-study
📝 [Paper] Studying pairing preferences between TCR alpha and beta chains
antigenomics/antigenomics.github.io
🌐 Immuno Sequencing Algorithms Group web page
antigenomics/bioinf-cov-classifier
Classifying the status of COVID samples and SARS-CoV2-specific TCRs
antigenomics/ilrfilter
Immunoglobulin-like Read Filter
antigenomics/pyigmap-old
A smart wrapper for V(D)J mapping software
antigenomics/tcr-thymic-selection
Network properties of public TCRs
antigenomics/hla-go-ms
HLA ligandome and parent protein Gene Ontology associations
antigenomics/mirpy
Python library and snippets for AIRR-seq data analysis, based on our in-house scripts
antigenomics/tcr-covid-classifier
TCR motifs associated with infectious conditions and HLAs
antigenomics/arradb
antigenomics/milib
⚙️ (internal) Milib library
antigenomics/milib_unused
MiLib: yet another Java library for Next Generation Sequencing (NGS) data processing
antigenomics/mir
A tool to handle immunogenomics data: from V/J references to AIRR-seq and TCR:pMHC structures.
antigenomics/repertoire-embedding
Analyzing network structure of the known TCR-cognate epitope map
antigenomics/repseqio
Utils for manipulations with RepSeq data. First step: utils to build V/D/J/C references.
antigenomics/tcr-survival-model
T-cell sampling and survival model for HSCT and similar T-cell repertoire dynamics studies
antigenomics/tcremp
T-cell receptor sequence embedding via prototypes
antigenomics/vdjdb-structure
🗂️ Template-based modelling of TCR:pMHC structures for VDJdb database
antigenomics/vdjdb-structure-tmp
Visualization of known and modeled structures from VDJdb using contact maps
antigenomics/vdjtrack
📝 Detecting T-cell expansion and quantifying clone survival from deep profiling of immune repertoires