jamieheather Goto Github PK
Name: Jamie Heather
Type: User
Bio: immunology | molecular biology | bioinformatics | Instructor in the MGH Center for Cancer Research
Blog: jamieheather.github.io
Name: Jamie Heather
Type: User
Bio: immunology | molecular biology | bioinformatics | Instructor in the MGH Center for Cancer Research
Blog: jamieheather.github.io
Convert TCR repertoires from AIRR-C to HLAGuessr format
Automatic DCR: a modified version of Decombinator for TCR annotation with automatic tag generation and allele-level output
Search the output of the Innate2Adaptive lab's Decombinator-based TCR analysis pipeline for MAIT (and other invariant TCR) cell sequences
Decombinator version 3, for error-correcting analysis of TCR repertoires
The tag and FASTA files which Decombinator v3 uses in its analysis of TCR repertoire data
Sample TCR FASTQ data for testing the Decombinator pipeline
Historical snapshots of the IMGT/GENE-DB immunoglobulin and T cell receptor germline database.
Python script to download (TCR) genes from IMGT/GENE-DB
Convert Adaptive Biotech's TCR files into the AIRR Community standard format
Compiled information about novel human T cell receptor alleles
Personal publication repository for the scientist James M. Heather
The python scripts used to run the analyses and produce the plots for the Heather et al study on photon vs proton induced lymphopenias
Misc utilities for receptor gene sequences
Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info
Analysis underlying the manuscript describing Stitchr, the Python tool for generating full-length TCR sequences
Scripts and files that I use to analyse T cell receptor repertoire data, produced by deep-sequencing
Extract reference and variant sequences for SNPs and other polymorphisms in the human T-cell receptor loci
A selection of scripts used in the analysis of data for my PhD thesis
Spreadsheet template files for 9x9 and 10x10 tube storage boxes for freezing biological samples
Testing the hypothesis that human cell lines grown as xenografts in mice recapitulate the HLA ligandomes of standard cultured cells.
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