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pQTLtools 0.2

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Accumulated changes

  • First release.
  • Depends R (>=3.5.0), pQTLdata
  • Import dplyr, gap, ggplot2
  • 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.