JamieHeather

stitchr

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

TubeStorageTemplates

Spreadsheet template files for 9x9 and 10x10 tube storage boxes for freezing biological samples

tcr-analysis

Scripts and files that I use to analyse T cell receptor repertoire data, produced by deep-sequencing

Decombinator

Decombinator version 3, for error-correcting analysis of TCR repertoires

immunoseq2airr

Convert Adaptive Biotech's TCR files into the AIRR Community standard format

stitchr-paper-analysis

Analysis underlying the manuscript describing Stitchr, the Python tool for generating full-length TCR sequences

IMGTgeneDL

Python script to download (TCR) genes from IMGT/GENE-DB

airrc2hlaguessr

Convert TCR repertoires from AIRR-C to HLAGuessr format

genedb-releases

Historical snapshots of the IMGT/GENE-DB immunoglobulin and T cell receptor germline database.

autoDCR

Automatic DCR: a modified version of Decombinator for TCR annotation with automatic tag generation and allele-level output

CheckMAIT

Search the output of the Innate2Adaptive lab's Decombinator-based TCR analysis pipeline for MAIT (and other invariant TCR) cell sequences

Decombinator-Tags-FASTAs

The tag and FASTA files which Decombinator v3 uses in its analysis of TCR repertoire data

Decombinator-Test-Data

Sample TCR FASTQ data for testing the Decombinator pipeline

istitchr-test

jamieheather.github.io

Personal publication repository for the scientist James M. Heather

novel-tcr-alleles

Compiled information about novel human T cell receptor alleles

old-pages

Personal publication repository for the scientist James M. Heather

receptor_utils

Misc utilities for receptor gene sequences

tcr-snps

Extract reference and variant sequences for SNPs and other polymorphisms in the human T-cell receptor loci

ThesisScripts

A selection of scripts used in the analysis of data for my PhD thesis

V-gene-polymorphisms

xenoimmunopeptidomics

Testing the hypothesis that human cell lines grown as xenografts in mice recapitulate the HLA ligandomes of standard cultured cells.