pQTLtools 0.2
Landmarks by date
- 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/
Accumulated changes
- First release.
- 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’).
- Suggest htmlwidgets, plotly.
- Suggest bookdown, cowplot, gap.datasets, httr, plyr, rmarkdown, Biobase, stringr.
- Suggest circlize, openxlsx, knitr and add HTML vignette (biomaRt, regioneR). with cis/trans-classification/ideogram/mhtplot2d examples.
- Suggest GenomicRanges & IRanges to handle >1MB region in regionqueries with wait=option.
- Replace ChangeLog with NEWS.md and generate vignette/articles with pkgdown.
- Invoke Roxygen2 for documentation.
- Add GitHub action
- Add inst/Bioconductor/.
- Add inst/STRING/change_STRING_colors.py.
- Add inst/UniProt|PPI/README.md.
- Add inst/snakemake
- Add pQTLtools.Rmd, bioconductor.Rmd, es.Rmd, snakemake.Rmd and SCALLOP-INF.Rmd articles.
- Add LICENSE.md and README.md.
- Add listed publications on pQTLs by Sun et al. (2018) and Suhre et al. (2020).
- Add run_TwoSampleMR(), make_ExpressionSet(), novelty_check(), qtl_lookup().
- Add pqtlMR() based on TwoSampleMR.
- Add run_coloc() based on coloc.
- Add import_OpenGWAS and therefore suggests gwasvcf, ieugwasr, rtracklayer, VariantAnnotation.
- Add import_eQTLCatalogue from eQTL-Catalogue-resources suggesting seqminer.
- Add genequries, regionqueries, snpqueries.
- Add uniprot2ids() based on UniProt.