Package: pafr 0.0.2

pafr: Read, Manipulate and Visualize 'Pairwise mApping Format' Data

Provides functions to read, process and visualize pairwise sequence alignments in the 'PAF' format used by 'minimap2' and other whole-genome aligners. 'minimap2' is described by Li H. (2018) <doi:10.1093/bioinformatics/bty191>.

Authors:David Winter [aut, cre], Kate Lee [ctb], Murray Cox [ctb]

pafr_0.0.2.tar.gz
pafr_0.0.2.zip(r-4.5)pafr_0.0.2.zip(r-4.4)pafr_0.0.2.zip(r-4.3)
pafr_0.0.2.tgz(r-4.4-any)pafr_0.0.2.tgz(r-4.3-any)
pafr_0.0.2.tar.gz(r-4.5-noble)pafr_0.0.2.tar.gz(r-4.4-noble)
pafr_0.0.2.tgz(r-4.4-emscripten)pafr_0.0.2.tgz(r-4.3-emscripten)
pafr.pdf |pafr.html✨
pafr/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/dwinter/pafr/issues

On CRAN:

7.07 score 67 stars 1 packages 59 scripts 255 downloads 1 mentions 14 exports 33 dependencies

Last updated 4 years agofrom:115d2b1be6. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winNOTENov 03 2024
R-4.5-linuxNOTENov 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:as_pafchrom_sizesdotplotfilter_secondary_alignmentsGb_labhighlight_queryhighlight_targetKb_labMb_labplot_coverageplot_syntenyread_bedread_paftheme_coverage_plot

Dependencies:clicolorspacedplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesstringistringrtibbletidyselectutf8vctrsviridisLitewithr

pafr: reading, manipulating and plotting genome alignments in the PAF format

David Winter

Rendered fromIntroduction_to_pafr.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2020-12-02
Started: 2019-09-26