jamieheather Goto Github PK

airrc2hlaguessr

Convert TCR repertoires from AIRR-C to HLAGuessr format

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

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

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

genedb-releases

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

imgtgenedl

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

immunoseq2airr

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

istitchr-test

jamieheather.github.io

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

stitchr

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

stitchr-paper-analysis

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

tcr-analysis

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

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

tubestoragetemplates

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

v-gene-polymorphisms

xenoimmunopeptidomics

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