Package: PCBS 0.1.1

PCBS: Principal Component BiSulfite

A system for fast, accurate, and flexible whole genome bisulfite sequencing (WGBS) data analysis of two-condition comparisons. Principal Component BiSulfite, 'PCBS', assigns methylated loci eigenvector values from the treatment-delineating principal component in lieu of running millions of pairwise statistical tests, which dramatically increases analysis flexibility and reduces computational requirements. Methods: <https://katlande.github.io/PCBS/articles/Differential_Methylation.html>.

Authors:Kathryn Lande [aut, cre, cph]

PCBS_0.1.1.tar.gz
PCBS_0.1.1.zip(r-4.5)PCBS_0.1.1.zip(r-4.4)PCBS_0.1.1.zip(r-4.3)
PCBS_0.1.1.tgz(r-4.4-any)PCBS_0.1.1.tgz(r-4.3-any)
PCBS_0.1.1.tar.gz(r-4.5-noble)PCBS_0.1.1.tar.gz(r-4.4-noble)
PCBS_0.1.1.tgz(r-4.4-emscripten)PCBS_0.1.1.tgz(r-4.3-emscripten)
PCBS.pdf |PCBS.html✨
PCBS/json (API)

# Install 'PCBS' in R:
install.packages('PCBS', repos = c('https://katlande.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/katlande/pcbs/issues

Datasets:
  • eigen - Simulated WGBS data for PCBS vignettes

On CRAN:

3.85 score 1 stars 194 downloads 24 exports 34 dependencies

Last updated 3 months agofrom:c26e14189d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winOKNov 03 2024
R-4.5-linuxOKNov 03 2024
R-4.4-winOKNov 03 2024
R-4.4-macOKNov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:addRanksCheckOvercompressioncheckRankchromDictchromDictMethDefineBestPCget_all_DMRsGet_Novel_DMRsgetPCRanksgetRegionScoreslinlmIntxMethyDiff_SetMethylDiffmethylDiff_metagenemultiple_metagenesOl_ReliableoneSeedplot_metagenerankDistscore_metagenesetilttrimDMR

Dependencies:clicolorspacedata.tabledplyrfansifarvergenericsggplot2ggrepelgluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalestibbletidyselectutf8vctrsviridisLitewithr