Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool). Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
| Version: | 1.1.2 |
| Depends: | R (≥ 3.3.0) |
| Imports: | data.table, ggplot2 (≥ 3.4), ggdendro, grid, gridExtra, grDevices, gtable, htmlTable, knitr (≥ 1.10), magrittr, methods, plyr, R6, R6P, RColorBrewer, reshape2, rlang, rmarkdown, rmzqc (≥ 0.5.0), seqinr, stats, utils, UpSetR, xml2, yaml |
| Suggests: | testthat |
| Published: | 2025-01-09 |
| DOI: | 10.32614/CRAN.package.PTXQC |
| Author: | Chris Bielow [aut, cre], Juliane Schmachtenberg [ctb], Swenja Wagner [ctb], Patricia Scheil [ctb], Tom Waschischek [ctb], Guido Mastrobuoni [dtc, rev] |
| Maintainer: | Chris Bielow <chris.bielow at bsc.fu-berlin.de> |
| BugReports: | https://github.com/cbielow/PTXQC/issues |
| License: | BSD_3_clause + file LICENSE |
| URL: | https://github.com/cbielow/PTXQC |
| NeedsCompilation: | no |
| SystemRequirements: | pandoc (http://pandoc.org) for building Vignettes and output reports as HTML |
| Citation: | PTXQC citation info |
| Materials: | README NEWS |
| In views: | Omics |
| CRAN checks: | PTXQC results |
| Reference manual: | PTXQC.pdf |
| Vignettes: |
Basic R-Usage Guide for PTXQC (source, R code) Customizing PTXQC reports (source) Drag'n'drop Usage Guide for PTXQC (source) Frequently asked questions for PTXQC (source) Input/Output data for PTXQC (source, R code) List of Metrics (source, R code) |
| Package source: | PTXQC_1.1.2.tar.gz |
| Windows binaries: | r-devel: PTXQC_1.1.2.zip, r-release: PTXQC_1.1.2.zip, r-oldrel: PTXQC_1.1.2.zip |
| macOS binaries: | r-release (arm64): PTXQC_1.1.2.tgz, r-oldrel (arm64): PTXQC_1.1.2.tgz, r-release (x86_64): PTXQC_1.1.2.tgz, r-oldrel (x86_64): PTXQC_1.1.2.tgz |
| Old sources: | PTXQC archive |
| Reverse imports: | RKorAPClient |
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