Package: RQdeltaCT 1.3.1

Daniel Zalewski

RQdeltaCT: Relative Quantification of Gene Expression using Delta Ct Methods

The commonly used methods for relative quantification of gene expression levels obtained in real-time PCR (Polymerase Chain Reaction) experiments are the delta Ct methods, encompassing 2^-dCt and 2^-ddCt methods, originally proposed by Kenneth J. Livak and Thomas D. Schmittgen (2001) <doi:10.1006/meth.2001.1262>. The main idea is to normalise gene expression values using endogenous control gene, present gene expression levels in linear form by using the 2^-(value)^ transformation, and calculate differences in gene expression levels between groups of samples (or technical replicates of a single sample). The 'RQdeltaCT' package offers functions that cover both methods for comparison of either independent groups of samples or groups with paired samples, together with importing expression datasets, performing multi-step quality control of data, enabling numerous data visualisations, enrichment of the standard workflow with additional useful analyses (correlation analysis, Receiver Operating Characteristic analysis, logistic regression), and conveniently export obtained results in table and image formats. The package has been designed to be friendly to non-experts in R programming.

Authors:Daniel Zalewski [aut, cre]

RQdeltaCT_1.3.1.tar.gz
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RQdeltaCT.pdf |RQdeltaCT.html✨
RQdeltaCT/json (API)

Peer review:

Bug tracker:https://github.com/donadelnal/rqdeltact/issues

On CRAN:

31 exports 1.51 score 157 dependencies 4 scripts 967 downloads

Last updated 20 days agofrom:1e4d3c68c1. Checks:OK: 7. Indexed: yes.

Exports:control_boxplot_genecontrol_boxplot_samplecontrol_cluster_genecontrol_cluster_samplecontrol_Ct_barplot_genecontrol_Ct_barplot_samplecontrol_pca_genecontrol_pca_samplecorr_genecorr_sampledelta_CtFCh_plotfilter_Ctfilter_transformed_datafind_ref_genelog_regmake_Ct_readynorm_finderparallel_plotpca_kmeansread_Ct_longread_Ct_wideresults_barplotresults_boxplotresults_heatmapresults_volcanoROChRQ_dCtRQ_ddCtsingle_pair_genesingle_pair_sample

Dependencies:askpassbackportsbase64encbitbit64blobbootbroombroom.helpersbslibcachemcallrcardscellrangercheckmateclicliprclustercodetoolscoincolorspaceconfintrconflictedcorrplotcpp11crayonctrlGenecurldata.tableDBIdbplyrdigestdplyrdtplyrevaluatefansifarverfastmapfontawesomeforcatsforeignFormulafsgarglegenericsGGallyggplot2ggpmiscggppggsignifggstatsgluegoogledrivegooglesheets4GPArotationgridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttridsisobandjquerylibjsonliteknitrlabelinglabelledlatticelibcoinlifecyclelmodel2lubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmimemnormtmodelrmodeltoolsmultcompmultcompViewmunsellmvtnormnlmennetoddsratioopensslpatchworkpheatmappillarpkgconfigplyrpolynomprettyunitspROCprocessxprogresspspsychpurrrquantregR6raggrappdirsRColorBrewerRcppreadrreadxlrematchrematch2reprexrlangrmarkdownrpartrstudioapirvestsandwichsassscalesselectrSparseMsplus2RstringistringrsurvivalsyssystemfontstextshapingTH.datatibbletidyrtidyselecttidyversetimechangetinytextzdbutf8uuidvctrsviridisviridisLitevroomwithrxfunxml2xtsyamlzoo