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Add TCRconvert and TCRconvertR tools to README #8

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slowkow merged 5 commits into from
Apr 24, 2025
Merged

Add TCRconvert and TCRconvertR tools to README #8

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69ce116
Add TCRconvert and TCRconvertR tools to README
emjbishop Apr 22, 2025
8d659fa
Update pRESTO link
emjbishop Apr 22, 2025
ed0a709
Update Allele Frequency Net link
emjbishop Apr 22, 2025
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Remove unsecure Allele Frequency Net link
emjbishop Apr 22, 2025
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add allelefrequencies.net link
slowkow Apr 24, 2025
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24 changes: 22 additions & 2 deletions README.md
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Expand Up @@ -313,7 +313,7 @@ Python package

https://presto.readthedocs.io/en/stable

https://bitbucket.org/kleinstein/presto
https://github.com/immcantation/presto

> pRESTO is a toolkit for processing raw reads from high-throughput sequencing of B cell and T cell repertoires.
>
Expand Down Expand Up @@ -379,6 +379,26 @@ https://github.com/emmijokinen/TCRconv

Jokinen E, Dumitrescu A, Huuhtanen J, Gligorijević V, Mustjoki S, Bonneau R, et al. [TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs.](https://pubmed.ncbi.nlm.nih.gov/36477794/) Bioinformatics. 2023;39. doi:10.1093/bioinformatics/btac788

### TCRconvert

Python package

https://github.com/seshadrilab/tcrconvert

> TCRconvert converts T cell receptor (TCR) gene names between the 10X, Adaptive, and IMGT naming conventions. It supports alpha-beta and gamma-delta TCRs for human, mouse, and rhesus macaque.

Manuscript in preparation.

### TCRconvertR

R package

https://github.com/seshadrilab/tcrconvertr

> TCRconvertR converts T cell receptor (TCR) gene names between the 10X, Adaptive, and IMGT naming conventions. It supports alpha-beta and gamma-delta TCRs for human, mouse, and rhesus macaque.

Manuscript in preparation.

### TCRGP

Python scripts
Expand Down Expand Up @@ -482,7 +502,7 @@ https://hla.alleles.org/nomenclature/index.html

### Allele Frequency Net Database

http://www.allelefrequencies.net/
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slowkow marked this conversation as resolved.
http://www.allelefrequencies.net/collaborators.asp

> AFND is a public resource that collects information on allele, genotype and haplotype frequencies from different polymorphic areas in the human genome such as human leukocyte antigens (HLA), killer-cell immunoglobulin-like receptors, etc. To produce this database we have compiled a large collection of datasets from different sources including: (i) peer-reviewed literature, (ii) datasets from international workshops in immunogenetics and histocompatiblity and (iii) data submitted directly to AFND by individual laboratories. As more than 75% of the submissions in AFND are derived from peer-review literature, we rely upon data verification by journal editors and reviewers when source studies are published.

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