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PTXQC  

Quality Report Generation for MaxQuant and mzTab Results
View on CRAN: Click here


Download and install PTXQC package within the R console
Install from CRAN:
install.packages("PTXQC")

Install from Github:
library("remotes")
install_github("cran/PTXQC")

Install by package version:
library("remotes")
install_version("PTXQC", "1.1.2")



Attach the package and use:
library("PTXQC")
Maintained by
Chris Bielow
[Scholar Profile | Author Map]
First Published: 2016-10-11
Latest Update: 2023-12-15
Description:
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) .
How to cite:
Chris Bielow (2016). PTXQC: Quality Report Generation for MaxQuant and mzTab Results. R package version 1.1.2, https://cran.r-project.org/web/packages/PTXQC. Accessed 11 Apr. 2025.
Previous versions and publish date:
0.80.13 (2016-10-11 12:42), 0.80.14 (2016-10-14 00:15), 0.82.2 (2017-02-17 18:31), 0.82.3 (2017-04-03 18:41), 0.82.5 (2017-05-04 17:36), 0.82.6 (2017-06-09 19:11), 0.90.0 (2017-08-05 01:30), 0.91.0 (2017-10-06 17:56), 0.92.0 (2017-10-14 00:15), 0.92.3 (2018-02-07 16:47), 0.92.4 (2019-02-08 11:13), 0.92.5 (2019-03-15 09:03), 0.92.6 (2019-04-16 16:02), 1.0.0 (2020-01-14 11:00), 1.0.1 (2020-02-02 17:40), 1.0.2 (2020-02-11 17:10), 1.0.4 (2020-03-28 20:30), 1.0.5 (2020-06-09 16:30), 1.0.7 (2020-11-12 12:00), 1.0.8 (2020-12-13 02:00), 1.0.9 (2021-02-03 11:30), 1.0.10 (2021-06-02 12:20), 1.0.11 (2021-10-04 10:30), 1.0.12 (2021-11-04 09:40), 1.0.13 (2022-03-22 17:20), 1.0.14 (2022-09-20 23:50), 1.0.15 (2023-04-25 23:50), 1.0.16 (2023-05-17 18:00), 1.0.17 (2023-07-11 01:40), 1.1.0 (2023-12-15 16:40), 1.1.1 (2024-03-11 20:50)
Other packages that cited PTXQC R package
View PTXQC citation profile
Other R packages that PTXQC depends, imports, suggests or enhances
Complete documentation for PTXQC
Functions, R codes and Examples using the PTXQC R package
Some associated functions: CV . CVDictionarySingleton . FilenameMapper-class . LCS . LCSn . MQDataReader-class . MzQCDateTime-class . MzQCanalysisSoftware-class . MzQCbaseQuality-class . MzQCcontrolledVocabulary-class . MzQCcvParameter-class . MzQCinputFile-class . MzQCmetadata-class . MzQCmzQC-class . MzQCqualityMetric-class . MzTabReader-class . NULL_to_NA . NULL_to_charNA . PTXQC . QCMetaFilenames . RSD . RTalignmentTree . ScoreInAlignWindow . YAMLClass-class . alignmentCheck . appendEnv . assembleMZQC . assignBlocks . boxplotCompare . brewer.pal.Safe . byX . byXflex . checkEnglishLocale . computeMatchRTFractions . correctSetSize . createReport . createYaml . darken . del0 . delLCP . delLCS . findAlignReference . fixCalibration . flattenList . fromDatatoMzQC . getAbundanceClass . getCVDictionary . getCVTemplate . getECDF . getFragmentErrors . getHTMLTable . getMQPARValue . getMaxima . getMetaData . getMetricsObjects . getPCA . getPeptideCounts . getProteinCounts . getQCHeatMap . getQualityMetricTemplate . getReportFilenames . getRunQualityTemplate . ggAxisLabels . ggText . grapes-plus-grapes . grepv . hasFileSuffix . idTransferCheck . inMatchWindow . isUndefined . isValidMzQC . lcpCount . lcsCount . longestCommonPrefix . longestCommonSuffix . mosaicize . parseOBO . pasten . pastet . peakSegmentation . peakWidthOverTime . plotTable . plotTableRaw . plot_CalibratedMSErr . plot_Charge . plot_ContEVD . plot_ContUser . plot_ContUserScore . plot_ContsPG . plot_CountData . plot_DataOverRT . plot_IDRate . plot_IDsOverRT . plot_IonInjectionTimeOverRT . plot_MBRAlign . plot_MBRIDtransfer . plot_MBRgain . plot_MS2Decal . plot_MS2Oversampling . plot_MissedCleavages . plot_RTPeakWidth . plot_RatiosPG . plot_ScanIDRate . plot_TIC . plot_TopN . plot_TopNoverRT . plot_UncalibratedMSErr . pointsPutX . print.PTXQC_table . printWithFooter . qcMetric-class . qcMetric_MSMSScans_TopNoverRT-class . qualBestKS . qualCentered . qualCenteredRef . qualGaussDev . qualHighest . qualLinThresh . qualMedianDist . qualUniform . read.MQ . removeSuffix . renameFile . repEach . scale01linear . scale_x_discrete_reverse . scale_y_discrete_reverse . shortenStrings . simplifyNames . suffixToCV . supCount . theme_blank . thinOut . thinOutBatch . wait_for_writable . writeMZQC . 
Some associated R codes: FilenameMapper.R . MQDataReader.R . MzQC_classes.R . MzTabReader.R . PTXQC.R . YAMLClass.R . createReport.R . createYaml.R . fcn_MQ.R . fcn_MQalign.R . fcn_PCA.R . fcn_QCHeat.R . fcn_misc.R . fcn_miscGGplot.R . fcn_mqpar.R . fcn_plots.R . fcn_qualities.R . mzQC.R . pkg_internal.R . qcMetric.R . qcMetric_EVD.R . qcMetric_MSMS.R . qcMetric_MSMSScans.R . qcMetric_PAR.R . qcMetric_PG.R . qcMetric_SM.R .  Full PTXQC package functions and examples
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