NEWS.md

In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

pQTLtools 0.4

(2024/10/18)

• Amend LocusZoom.js.Rmd.
• Unify DESCRIPTION/README (finally!).
• Add SummarizedExperiment section to es.Rmd --> esse.Rmd.
• Add csq(), protein_altering_variants (so data/), histo.fyi, aria-label.
• Adopt new hg38 LD blocks for turboman().
• Add spectrum.Rmd.
• Renew call to ldops in novelty_check() in accordance with ieugwasr.
• Replace tests/ with most recent PROC results.

pQTLtools 0.3

(2024/05/26)

• Activate package logo for the GitHub repository.
• Dedicated .R files for (blocks of) functions.
• Use of scope operator for clarification, e.g., ensembldb::genes().
• Use of OPENGWAS_JWT from https://api.opengwas.io/profile/.
• Suggest IlluminaHumanMethylation450kmanifest, OUTRIDER.
• Fix URL in DESCRIPTION/snakemake.Rmd.

pQTLtools 0.2

(2024/04/24)

Milestones

• 2023.12. Add LocusZoom.js article.
• 2023.05. Test data are fully available with medRxiv post of the SCALLOP paper.
• 2022.12. A new package pQTLdata is created to hold panel and meta data.
• 2022.06. It passes CRAN checks with no warning.
• 2021.02. A web-driven documentation is now available, https://jinghuazhao.github.io/pQTLtools/.

Package

The information here mirrors the package DESCRIPTION,

• Depends R (>=3.5.0), pQTLdata.
• Import dplyr, gap, ggplot2, Rdpack.
• importFrom utils read.table tail.
• Import from lmm as template, use save(compress='xz').
• Replace ChangeLog with NEWS.md.
• LICENSE.md and README.md.
• Reduce size by sed -i '/ISSN/d' REFERENCES.bib.
• Suggest Biobase, BioStrings, GenomeInfoDb, GenomicRanges, IRanges, VariantAnnotation.
• Suggest Roxygen2.
• Suggest biomaRt, bookdown, circlize, cowplot.
• Suggest gap.datasets, gwasvcf, htmlwidgets, httr, ieugwasr.
• Suggest knitr, mclust, meta.
• Suggest openxlsx, plotly, plyr.
• Suggest regione, rgl, rmarkdown, rtracklayer.
• Suggest scatterplot3d, seqminer, stringr.
• GitHub action
• inst/Bioconductor/.
• inst/STRING/change_STRING_colors.py.
• inst/UniProt|PPI/README.md.
• inst/snakemake
• pQTLtools.Rmd, bioconductor.Rmd, es.Rmd, LocusZoom.js.Rmd, snakemake.Rmd and SCALLOP-INF.Rmd articles.
• List publications on pQTLs by Sun et al. (2018) and Suhre et al. (2020).

Functions

The list is in no particular order,

• peptideMapping(), peptideAssociationPlot().
• make_ExpressionSet(), novelty_check(), qtl_lookup(), turboman(), turboqq().
• Reflow turboman.r/[partial]turboqq.r by formatR::tidy_source().
• pqtlMR(), run_TwoSampleMR().
• run_coloc().
• import_OpenGWAS()
• import_eQTLCatalogue().
• genequries(), regionqueries(), snpqueries().
• uniprot2ids().

pQTLtools 0.1

• First release

jinghuazhao/pQTLtools documentation built on Oct. 22, 2024, 12:56 a.m.