diff --git a/README.Rmd b/README.Rmd index 5c90bb8..b26db0d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -93,7 +93,8 @@ Additionally, you can also cite the `hlabud` package like this: - Slowikowski K. hlabud: HLA analysis in R. Zenodo. https://doi.org/10.5281/zenodo.11093557 -# Related work + +# Learn more I recommend this article for anyone new to HLA, because the beautiful figures help to build intuition: @@ -104,12 +105,12 @@ Learn about the conventions for HLA nomenclature: - Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, et al. [Nomenclature for factors of the HLA system, 2010.](https://pubmed.ncbi.nlm.nih.gov/20356336/) Tissue Antigens. 2010;75: 291–455. -[HATK] is set of Python scripts for processing and analyzing IMGT-HLA data. -Here is the related article: -- Choi W, Luo Y, Raychaudhuri S, Han B. [HATK: HLA analysis toolkit](https://pubmed.ncbi.nlm.nih.gov/32735319). Bioinformatics. 2021;37: 416–418. doi:10.1093/bioinformatics/btaa684 +# Related work -[HATK]: https://github.com/WansonChoi/HATK +[HLAtools] is an R package that also makes IPD-IMGT/HLA resources available for analysis, and also works with BIGDAWG data formats. + +[HLAtools]: https://github.com/sjmack/HLAtools For case-control analysis of HLA genotype data, consider the [BIGDAWG](https://CRAN.R-project.org/package=BIGDAWG) R package available on @@ -117,6 +118,19 @@ CRAN. Here is the related article: - Pappas DJ, Marin W, Hollenbach JA, Mack SJ. [Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): An integrated case-control analysis pipeline.](https://pubmed.ncbi.nlm.nih.gov/26708359) Hum Immunol. 2016;77: 283–287. +[HATK] is set of Python scripts for processing and analyzing IMGT-HLA data. +Here is the related article: + +- Choi W, Luo Y, Raychaudhuri S, Han B. [HATK: HLA analysis toolkit.](https://pubmed.ncbi.nlm.nih.gov/32735319) Bioinformatics. 2021;37: 416–418. doi:10.1093/bioinformatics/btaa684 + +[HATK]: https://github.com/WansonChoi/HATK + +The HLA divergence code in hlabud is a translation of the +[original Perl code](https://sourceforge.net/projects/granthamdist) by +[Tobias Lenz](https://orcid.org/0000-0002-7203-0044), which was published in: + +- Pierini F, Lenz TL. [Divergent allele advantage at human MHC genes: signatures of past and ongoing selection.](https://pubmed.ncbi.nlm.nih.gov/29893875) Mol Biol Evol. 2018. doi:10.1093/molbev/msy116 + [HLAdivR] is another R package for calculating HLA divergence. [HLAdivR]: https://github.com/rbentham/HLAdivR/ diff --git a/README.md b/README.md index c53e030..cf0a317 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ a <- hla_alignments("DRB1") a$release ``` - ## [1] "3.56.0" + ## [1] "3.59.0" ``` r dosage(a$onehot, c("DRB1*03:01:05", "DRB1*03:02:03")) @@ -39,7 +39,7 @@ n <- hla_alignments("DRB1", type = "nuc") n$release ``` - ## [1] "3.56.0" + ## [1] "3.59.0" ``` r dosage(n$onehot, c("DRB1*03:01:05", "DRB1*03:02:03")) @@ -124,7 +124,7 @@ Additionally, you can also cite the `hlabud` package like this: - Slowikowski K. hlabud: HLA analysis in R. Zenodo. -# Related work +# Learn more I recommend this article for anyone new to HLA, because the beautiful figures help to build intuition: @@ -141,12 +141,11 @@ Learn about the conventions for HLA nomenclature: 2010.](https://pubmed.ncbi.nlm.nih.gov/20356336/) Tissue Antigens. 2010;75: 291–455. -[HATK](https://github.com/WansonChoi/HATK) is set of Python scripts for -processing and analyzing IMGT-HLA data. Here is the related article: +# Related work -- Choi W, Luo Y, Raychaudhuri S, Han B. [HATK: HLA analysis - toolkit](https://pubmed.ncbi.nlm.nih.gov/32735319). Bioinformatics. - 2021;37: 416–418. +[HLAtools](https://github.com/sjmack/HLAtools) is an R package that also +makes IPD-IMGT/HLA resources available for analysis, and also works with +BIGDAWG data formats. For case-control analysis of HLA genotype data, consider the [BIGDAWG](https://CRAN.R-project.org/package=BIGDAWG) R package @@ -157,5 +156,21 @@ available on CRAN. Here is the related article: analysis pipeline.](https://pubmed.ncbi.nlm.nih.gov/26708359) Hum Immunol. 2016;77: 283–287. +[HATK](https://github.com/WansonChoi/HATK) is set of Python scripts for +processing and analyzing IMGT-HLA data. Here is the related article: + +- Choi W, Luo Y, Raychaudhuri S, Han B. [HATK: HLA analysis + toolkit.](https://pubmed.ncbi.nlm.nih.gov/32735319) Bioinformatics. + 2021;37: 416–418. + +The HLA divergence code in hlabud is a translation of the [original Perl +code](https://sourceforge.net/projects/granthamdist) by [Tobias +Lenz](https://orcid.org/0000-0002-7203-0044), which was published in: + +- Pierini F, Lenz TL. [Divergent allele advantage at human MHC genes: + signatures of past and ongoing + selection.](https://pubmed.ncbi.nlm.nih.gov/29893875) Mol Biol + Evol. 2018. + [HLAdivR](https://github.com/rbentham/HLAdivR/) is another R package for calculating HLA divergence.