Package: qPLEXanalyzer 1.25.0

Ashley Sawle

qPLEXanalyzer: Tools for quantitative proteomics data analysis

Tools for TMT based quantitative proteomics data analysis.

Authors:Matthew Eldridge [aut], Kamal Kishore [aut], Ashley Sawle [aut, cre]

qPLEXanalyzer_1.25.0.tar.gz
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qPLEXanalyzer.pdf |qPLEXanalyzer.html✨
qPLEXanalyzer/json (API)
NEWS

# Install 'qPLEXanalyzer' in R:

install.packages('qPLEXanalyzer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/crukci-bioinformatics/qplexanalyzer/issues

Datasets:

ER_ARID1A_KO_MCF7 - ER_ARID1A_KO_MCF7 dataset
exp2_Xlink - Exp2_Xlink dataset
exp3_OHT_ESR1 - Exp3_OHT_ESR1 dataset
human_anno - Human_anno dataset
mouse_anno - Mouse_anno dataset

On BioConductor:qPLEXanalyzer-1.25.0(bioc 3.21)qPLEXanalyzer-1.24.0(bioc 3.20)

immunooncology proteomics massspectrometry normalization preprocessing qualitycontrol dataimport

4.08 score 1 stars 9 scripts 216 downloads 6 mentions 24 exports 138 dependencies

Last updated 4 months agofrom:9825be7add. Checks:2 ERROR, 6 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Jan 30 2025
R-4.5-win	WARNING	Jan 30 2025
R-4.5-mac	WARNING	Jan 30 2025
R-4.5-linux	ERROR	Jan 30 2025
R-4.4-win	WARNING	Jan 30 2025
R-4.4-mac	WARNING	Jan 30 2025
R-4.3-win	WARNING	Jan 30 2025
R-4.3-mac	WARNING	Jan 30 2025

Exports:assignColours coefVar computeDiffStats convertToMSnset corrPlot coveragePlot getContrastResults groupScaling hierarchicalPlot intensityBoxplot intensityPlot IRSnorm maVolPlot mergePeptides mergeSites normalizeQuantiles normalizeScaling pcaPlot peptideIntensityPlot plotMeanVar regressIntensity rliPlot rowScaling summarizeIntensities

Dependencies:abind affy affyio AnnotationFilter askpass assertthat base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel Biostrings bit bit64 bslib cachem cli clipr clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DelayedArray digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggdendro ggplot2 glue gtable highr hms htmltools htmlwidgets httr igraph impute IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle limma magrittr MALDIquant MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MsCoreUtils MSnbase MultiAssayExperiment munsell mzID mzR ncdf4 nlme openssl pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch purrr QFeatures R6 rappdirs RColorBrewer Rcpp readr reshape2 Rhdf5lib rlang rmarkdown S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom vsn withr xfun XML XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for qPLEX-RIME data analysis	qPLEXanalyzer-package qPLEXanalyzer
Assigns colours to samples in groups	assignColours
Calculating the coefficient of variation by utilizing expression data within individual sample groups.	coefVar
Compute differential statistics	computeDiffStats
Converts proteomics TMT intensity data to MSnSet	convertToMSnset
Correlation plot	corrPlot
Plot peptide sequence coverage	coveragePlot
ER_ARID1A_KO_MCF7 dataset	ER_ARID1A_KO_MCF7
exp2_Xlink dataset	exp2_Xlink
exp3_OHT_ESR1 dataset	exp3_OHT_ESR1
Get differential statistics results	getContrastResults
Normalization by scaling within group	groupScaling
Hierarchical clustering plot	hierarchicalPlot
human_anno dataset	human_anno
Intensity Distribution boxplot	intensityBoxplot
Intensity Distribution Plot	intensityPlot
Batch Correction by Internal Reference Scale	IRSnorm
MA or Volcano Plot	maVolPlot
Merge identical modified peptides intensities	mergePeptides
Merge identical modification sites intensities	mergeSites
mouse_anno dataset	mouse_anno
Quantile normalization	normalizeQuantiles
Normalization by scaling	normalizeScaling
PCA plot	pcaPlot
Plot peptide intensities	peptideIntensityPlot
Mean variance plot	plotMeanVar
Regression based analysis	regressIntensity
Relative log intensity plot	rliPlot
Normalization by scaling peptide/protein intensity across all samples	rowScaling
Summarizes peptides intensities to proteins	summarizeIntensities

Usage by other packages (reverse dependencies)