Package: PTXQC 1.1.1
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Chris Bielow
PTXQC: Quality Report Generation for MaxQuant and mzTab Results
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>.
Authors:
PTXQC_1.1.1.tar.gz
PTXQC_1.1.1.zip(r-4.5)PTXQC_1.1.1.zip(r-4.4)PTXQC_1.1.1.zip(r-4.3)
PTXQC_1.1.1.tgz(r-4.5-any)PTXQC_1.1.1.tgz(r-4.4-any)PTXQC_1.1.1.tgz(r-4.3-any)
PTXQC_1.1.1.tar.gz(r-4.5-noble)PTXQC_1.1.1.tar.gz(r-4.4-noble)
PTXQC_1.1.1.tgz(r-4.4-emscripten)PTXQC_1.1.1.tgz(r-4.3-emscripten)
PTXQC.pdf |PTXQC.html✨
PTXQC/json (API)
NEWS
# Install 'PTXQC' in R: |
install.packages('PTXQC', repos = c('https://cbielow.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cbielow/ptxqc/issues
drag-and-drophacktoberfestheatmapmatch-between-runsmaxquantmetricmztabopenmsproteomicsquality-controlquality-metricsreport
Last updated 11 months agofrom:41ea336a44. Checks:8 OK. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Feb 05 2025 |
R-4.5-win | OK | Feb 05 2025 |
R-4.5-mac | OK | Feb 05 2025 |
R-4.5-linux | OK | Feb 05 2025 |
R-4.4-win | OK | Feb 05 2025 |
R-4.4-mac | OK | Feb 05 2025 |
R-4.3-win | OK | Feb 05 2025 |
R-4.3-mac | OK | Feb 05 2025 |
Exports:assembleMZQCassignBlocksboxplotComparebyXbyXflexcorrectSetSizecreateReportcreateYamldelLCPdelLCSFilenameMappergetECDFgetFragmentErrorsgetHTMLTablegetMaximagetMQPARValuegetPCAgetReportFilenamesgrepvlcpCountLCSlcsCountLCSnlongestCommonPrefixlongestCommonSuffixmodsToTablemodsToTableByRawmosaicizepastenpastetpeakWidthOverTimeplot_CalibratedMSErrplot_Chargeplot_ContEVDplot_ContsPGplot_ContUserplot_ContUserScoreplot_CountDataplot_DataOverRTplot_IDRateplot_IDsOverRTplot_IonInjectionTimeOverRTplot_MBRAlignplot_MBRgainplot_MBRIDtransferplot_MissedCleavagesplot_MS2Decalplot_MS2Oversamplingplot_peptideModsplot_RatiosPGplot_RTPeakWidthplot_ScanIDRateplot_TICplot_TopNplot_TopNoverRTplot_UncalibratedMSErrplotTablepointsPutXQCMetaFilenamesqcMetricqualBestKSqualCenteredqualCenteredRefqualGaussDevqualHighestqualLinThreshqualMedianDistqualUniformread.MQrenameFilerepEachRTalignmentTreeshortenStringssimplifyNamessupCounttheme_blankYAMLClass
Dependencies:ade4backportsbase64encbriobslibcachemcallrcheckmateclicollectionscolorspacecpp11crayoncurldata.tabledescdiffobjdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggdendroggplot2gluegridExtragtablehighrhtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonlitejsonvalidateknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeontologyIndexpillarpixmappkgbuildpkgconfigpkgloadplyrpraiseprocessxpspurrrR6R6PrappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownrmzqcrprojrootrstudioapisassscalessegmentedseqinrspstringistringrtestthattibbletidyrtidyselecttinytexUpSetRutf8V8vctrsviridisLitewaldowithrxfunxml2yaml
Basic R-Usage Guide for PTXQC
Rendered fromPTXQC-Basic_Guide_for_R_users.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2020-01-16
Started: 2015-10-20
Customizing PTXQC reports
Rendered fromPTXQC-CustomizeReport.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2020-11-11
Started: 2015-10-20
Drag'n'drop Usage Guide for PTXQC
Rendered fromPTXQC-DragNDrop.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2017-04-03
Started: 2015-10-20
Frequently asked questions for PTXQC
Rendered fromPTXQC-FAQ.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2017-05-04
Started: 2015-11-19
Input/Output data for PTXQC
Rendered fromPTXQC-Input_And_Output_Data.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2023-05-17
Started: 2015-11-01
List of Metrics
Rendered fromPTXQC-ListOfMetrics.Rmd
usingknitr::rmarkdown
on Feb 05 2025.Last update: 2023-12-16
Started: 2018-02-07