tcr-repertoire

There are 2 repositories under tcr-repertoire topic.

• 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 291

• sidhomj / DeepTCR

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

  adaptive-immunitydeep-learningimmunologyrepertoiretcrtcr-repertoire
  Language:Jupyter Notebook 109

• 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

• GuoBioinfoLab / CATT

  An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

  tcrtcr-repertoirebioinformaticsbioinformatics-tool
  Language:Julia 18

• mehdiborji / nanoranger

  simplified cellranger for long-read data

  cellrangerminimap2mixcrnanorangersc-rna-seqsingle-cell-rna-seqspatial-transcriptomicstcr-repertoiretcr-seqvdj-recombination10x-genomicspacbioslide-seqbioinformaticsbioinformatics-pipelinecomputational-genomicscomputational-sciencelinuxpython3
  Language:Python 13

• Lee-CBG / catELMo

  catELMo: Context-Aware Amino Acid Embedding Advances Analysis of TCR-Epitope Interactions

  amino-acid-encodinglanguage-modeltcr-epitopetcr-repertoire
  Language:Python 11

• GuoBioinfoLab / TCRdb

  A database of T-cell receptor sequences

  tcrtcr-repertoiredatabasebioinformatics
  Language:Python 6
• IgGeneUsage

  snaketron / IgGeneUsage

  Comparison of gene usage in immune repertoires under different biological conditions

  immune-repertoiresdifferential-gene-expressionhigh-throughput-sequencingimmunoinformaticsimmunological-bioinformaticsvdj-recombinationdifferential-analysistcr-repertoirebcr-repertoireb-cell-receptorimmunologyimmunoglobulinimmunogenomicsimmune-repertoireimmune-repertoire-analysis
  Language:R 6

• hillarykoch / powerTCR

  R package. Main goals are to fit models to the clone size distribution of the TCR repertoire, and to perform model-based comparative analysis of samples.

  clusteringtcr-repertoireextremes
  Language:R 5

• abcwcm / GeartySchietinger

  Scripts related to bulkRNA-seq as well as single-cell CITE-seq and VDJ-seq data of Gearty et al. (2021)

  single-cellrna-seqcite-seqtcr-repertoire
  Language:HTML 4

• dyohanne / RepAn

  Analysis functions for deep sequenced immune repertoire (Repseq) datasets in R

  immunoinformaticsdifferential-abundance-analysestcr-repertoiretcrtcrbbioinformaticsbioinformatics-pipelinerepseq
  Language:R 3

• immunomind / slides

  Slides for presentations by ImmunoMind team

  bcr-repertoirebioinformaticsdeep-learningimmunoinformaticsimmunologymachine-learningpresentation-slidestcr-repertoire
  3

• pwwang / immunopipe-example

  An example of immunopipe

  immunotherapyseuratsingle-cell-analysissingle-cell-rna-seqtcrtcr-repertoire
  Language:HTML 2

• pughlab / ped_CapTCRseq

  Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation

  mixcrngspediatric-cancertcr-repertoire
  Language:Jupyter Notebook 1

• BenNicolet / TCR_clonality_analysis

  TCR clonotype analysis using mixcr and immunarch.

  tcr-repertoiremixcrimmunology
  Language:Shell 0

• DKruttika / HPC-GPU-projects

  Code for HRDetect, image analysis, TCR - seq from HGSOC samples

  bigwigshovernettcr-repertoire
  Language:Python 0

• fanzhanglab / TteK

  Code for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated CD8 T cells.

  immunogenomicsinflammationrheumatoid-arthritissingle-cell-omicstcelltcr-repertoire
  Language:Jupyter Notebook 0

• LedaKatopodi / library-of-cheatsheets

  📑 A library of example code -aka cheatsheets- for tools I use or analyses I carry out pretty often. This repo doubles as an easy way to find the code I need without going through all my scripts.

  bioinformaticscheatsheetsrna-seqtcr-repertoirevisualizationwhole-exome-sequencing
  Language:Shell 0

• yanismiraoui / M4R-Project-Notebooks

  Deep unsupervised learning methods for the identification and characterization of TCR specificity to Sars-Cov-2

  antigenautoencodersbioinformaticsdeep-learningneural-networkssars-cov-2specificitytcrtcr-repertoiretcr-bert
  Language:Jupyter Notebook 0

• adiamb / Narcolepsy_immunology_2018

  Scripts used in the manuscript titled "Autoimmunity to hypocretin and molecular mimicry to flu in Type 1 narcolepsy"

  tcr-repertoireflusingle-cell
  Language:Python

• oicr-gsi / trust4

  analysis of antibody diversity, .wdl wrapper workflow

  immunitytcr-repertoirebcr-repertoire
  Language:WDL

• pughlab / iMATRIX-Atezo_Biomarker

  Multimodal immunogenomic biomarker analysis of tumours from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

  biomarkersimmunoinformaticsimmunotherapyngspediatric-cancertcr-repertoire
  Language:Jupyter Notebook