Package: protGear 1.11.0

Kennedy Mwai

protGear: Protein Micro Array Data Management and Interactive Visualization

A generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance.These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

Authors:Kennedy Mwai [cre, aut], James Mburu [aut], Jacqueline Waeni [ctb]

protGear_1.11.0.tar.gz
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protGear_1.11.0.tgz(r-4.4-any)protGear_1.11.0.tgz(r-4.3-any)
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protGear.pdf |protGear.html✨
protGear/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/keniajin/protgear/issues

On BioConductor:protGear-1.11.0(bioc 3.21)protGear-1.10.0(bioc 3.20)

microarrayonechannelpreprocessingbiomedicalinformaticsproteomicsbatcheffectnormalizationbayesianclusteringregressionsystemsbiologyimmunooncologybackground-correctionmicroarray-datanormalisationproteomics-datashinyshinydashboard

4.30 score 1 stars 6 scripts 258 downloads 28 exports 177 dependencies

Last updated 2 months agofrom:97e8c52637. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 30 2024
R-4.5-winNOTENov 30 2024
R-4.5-linuxNOTENov 30 2024
R-4.4-winNOTENov 30 2024
R-4.4-macNOTENov 30 2024
R-4.3-winNOTENov 30 2024
R-4.3-macNOTENov 30 2024

Exports:array_varsbest_CV_estimationbg_correctbuffer_spotscheck_sampleID_filescreate_dircv_by_sample_estimationcv_estimationextract_bglaunch_protGear_interactivelaunch_selectmatrix_normalisemerge_sampleIDminpositivename_of_filesoutput_trend_statsplot_bgplot_bufferplot_FBplot_normalisedplot_normalised_antigenread_array_filesread_array_visualizerlm_normaliserlm_normalise_matrixtag_subtractvisualize_slidevisualize_slide_2d

Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobbootbroombslibcachemcarcarDataclicliprclustercolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdendextendDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustflexdashboardfontawesomeforcatsFormulafsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGGallyggplot2ggpubrggrepelggsciggsignifggstatsgluegridExtragtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTKendallknitrlabelinglaterlatticelazyevalleapslifecyclelimmalme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpheatmappillarpkgconfigplogrplotlyplyrpngpolynompreprocessCoreprettyunitsprogresspromisespurrrquantregR.cacheR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenreadrremotesreshape2rlangrmarkdownrprojrootRSQLiterstatixS4Vectorssassscalesscatterplot3dshinyshinydashboardsourcetoolsSparseMstatmodstringistringrstylersurvivalsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisviridisLitevroomvsnwithrxfunXMLxtableXVectoryamlzlibbioc

protGear vignette processing suite

Kennedy Mwai

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2022-12-11
Started: 2021-07-01