diff --git a/README.Rmd b/README.Rmd index 702b780..5c90bb8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -13,6 +13,7 @@ output: # hlabud [![R-CMD-check](https://github.com/slowkow/hlabud/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/slowkow/hlabud/actions/workflows/R-CMD-check.yaml) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11093557.svg)](https://doi.org/10.5281/zenodo.11093557) hlabud provides methods to retrieve sequence alignment data from [IMGTHLA] and convert the data into convenient R matrices ready for downstream analysis. See the [usage examples](https://slowkow.github.io/hlabud/articles/examples.html) to learn how to use the data with logistic regression and dimensionality reduction. We also share tips on how to [visualize the 3D molecular structure](https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html) of HLA proteins and highlight specific amino acid residues. @@ -90,7 +91,7 @@ See the [usage examples](https://slowkow.github.io/hlabud/articles/examples.html Additionally, you can also cite the `hlabud` package like this: -- Slowikowski K. hlabud: methods for access and analysis of the human leukocyte antigen (HLA) gene sequence alignments from IMGT/HLA. R package version 1.0.0. +- Slowikowski K. hlabud: HLA analysis in R. Zenodo. https://doi.org/10.5281/zenodo.11093557 # Related work @@ -116,5 +117,7 @@ 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. +[HLAdivR] is another R package for calculating HLA divergence. + +[HLAdivR]: https://github.com/rbentham/HLAdivR/ -https://github.com/rbentham/HLAdivR/ diff --git a/README.md b/README.md index 33a59d8..c53e030 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # hlabud [![R-CMD-check](https://github.com/slowkow/hlabud/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/slowkow/hlabud/actions/workflows/R-CMD-check.yaml) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11093557.svg)](https://doi.org/10.5281/zenodo.11093557) hlabud provides methods to retrieve sequence alignment data from [IMGTHLA](https://github.com/ANHIG/IMGTHLA) and convert the data into @@ -120,9 +121,8 @@ please cite the AFND paper: Additionally, you can also cite the `hlabud` package like this: -- Slowikowski K. hlabud: methods for access and analysis of the human - leukocyte antigen (HLA) gene sequence alignments from IMGT/HLA. R - package version 1.0.0. +- Slowikowski K. hlabud: HLA analysis in R. Zenodo. + # Related work @@ -157,4 +157,5 @@ available on CRAN. Here is the related article: analysis pipeline.](https://pubmed.ncbi.nlm.nih.gov/26708359) Hum Immunol. 2016;77: 283–287. - +[HLAdivR](https://github.com/rbentham/HLAdivR/) is another R package for +calculating HLA divergence. diff --git a/index.Rmd b/index.Rmd index 097d193..f109c3a 100644 --- a/index.Rmd +++ b/index.Rmd @@ -16,7 +16,7 @@ dosage(a$onehot, c("DRB1*03:01:05", "DRB1*03:02:03")) ``` From this output, we can conclude that four positions (26, 28, 47, 86) distinguish these two HLA-DRB1 alleles. -We see that DRB1\*03:01:05 has a F at position 26 and DRB1\*03:02:03 has a Y. +We see that DRB1\*03:01:05 has a Y at position 26 and DRB1\*03:02:03 has a F. Installation diff --git a/index.md b/index.md index 8f7fb95..96bb614 100644 --- a/index.md +++ b/index.md @@ -21,7 +21,7 @@ What amino acid positions are different between these two genotypes? From this output, we can conclude that four positions (26, 28, 47, 86) distinguish these two HLA-DRB1 alleles. We see that DRB1\*03:01:05 has a -F at position 26 and DRB1\*03:02:03 has a Y. +Y at position 26 and DRB1\*03:02:03 has a F. # Installation diff --git a/vignettes/articles/examples_files/figure-html/umap-2digit-1.png b/vignettes/articles/examples_files/figure-html/umap-2digit-1.png index a66fac8..09fc57f 100644 Binary files a/vignettes/articles/examples_files/figure-html/umap-2digit-1.png and b/vignettes/articles/examples_files/figure-html/umap-2digit-1.png differ diff --git a/vignettes/articles/examples_files/figure-html/umap-57-1.png b/vignettes/articles/examples_files/figure-html/umap-57-1.png index bde661f..3160652 100644 Binary files a/vignettes/articles/examples_files/figure-html/umap-57-1.png and b/vignettes/articles/examples_files/figure-html/umap-57-1.png differ diff --git a/vignettes/articles/examples_files/figure-html/umap-D57-1.png b/vignettes/articles/examples_files/figure-html/umap-D57-1.png index 99d6be7..8cb419a 100644 Binary files a/vignettes/articles/examples_files/figure-html/umap-D57-1.png and b/vignettes/articles/examples_files/figure-html/umap-D57-1.png differ