Package: RVA 0.0.4

RVA: RNAseq Visualization Automation

Automate downstream visualization & pathway analysis in RNAseq analysis. 'RVA' is a collection of functions that efficiently visualize RNAseq differential expression analysis result from summary statistics tables. It also utilize the Fisher's exact test to evaluate gene set or pathway enrichment in a convenient and efficient manner.

Authors:Xingpeng Li [aut, cre]

RVA_0.0.4.tar.gz
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RVA.pdf |RVA.html✨
RVA/json (API)

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

Bug tracker:https://github.com/thermostats/rva/issues

Datasets:

On CRAN:

Conda:

5.65 score 9 stars 6 scripts 281 downloads 27 mentions 8 exports 209 dependencies

Last updated 3 years agofrom:dbdf9b4f3e. Checks:1 OK, 1 ERROR, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 09 2025
R-4.5-winNOTEMar 09 2025
R-4.5-macNOTEMar 09 2025
R-4.5-linuxNOTEMar 09 2025
R-4.4-winNOTEMar 09 2025
R-4.4-macNOTEMar 09 2025
R-4.4-linuxNOTEMar 09 2025
R-4.3-winNOTEDec 09 2024
R-4.3-macERRORDec 09 2024

Exports:plot_cutoffplot_geneplot_heatmap.cfbplot_heatmap.cpmplot_heatmap.exprplot_pathwayplot_qqplot_volcano

Dependencies:abindannotateAnnotationDbiapeaplotaskpassbabelgenebackportsbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacirclizeclicliprclueclusterclusterProfilercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArrayDerivdigestdoBydoParallelDOSEdplyredgeRenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeforcatsforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggforceggfunggnewscaleggplot2ggplotifyggpubrggrepelggsciggsignifggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgraphgridExtragridGraphicsGSEABasegsonGSVAdatagtablehavenhgu95a.dbhighrhmshtmltoolshtmlwidgetshttrigraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4locfitlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmsigdbrmunsellnlmenloptrnnetnumDerivopensslorg.Hs.eg.dbpatchworkpbkrtestpillarpkgconfigplogrplotlyplyrpngpolyclippolynomprettyunitsprogresspromisespurrrquantregqvalueR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreadrreformulasreshape2rjsonrlangrmarkdownRSQLiterstatixrWikiPathwaysS4ArraysS4VectorssassscalesscatterpieshapesnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidyrtidyselecttidytreetimechangetinytextreeiotweenrtzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlyulab.utils

RNAseq Visualization Automation

Rendered fromRVA.Rmdusingknitr::rmarkdownon Mar 09 2025.

Last update: 2021-02-10
Started: 2020-08-17

Readme and manuals

Help Manual

Help pageTopics
This is data to be included in packagec2BroadSets
calculate pathway scorescal.pathway.scores
Calculate CFBcalc.cfb
This is data to be included in packagecount_table
DL Pathways DBdlPathwaysDB
Get CPM Colorsget.cpm.colors
Create ggplot object for number of differntially expressed genes with different FDR and fold change cutoff.get.cutoff.df
Create ggplot object for number of differntially expressed genes with different FDR and fold change cutoff.get.cutoff.ggplot
Create plotly object for number of DE genes at different cutoff combinationsmake.cutoff.plotly
Multi PlotmultiPlot
Null Returnnullreturn
Check number of DE genes at different cutoff combinationsplot_cutoff
Create plotly object for number of DE genes at different cutoff combinationsplot_cutoff_single
Plot gene expressionplot_gene
Plot a CFB Heatmapplot_heatmap.cfb
Plot a CPM Heatmapplot_heatmap.cpm
Plot Heatmap From Raw CPMplot_heatmap.expr
Pathway analysis and visualizationplot_pathway
Plot qqplotplot_qq
Plot volcanoplotplot_volcano
Pretty GraphsprettyGraphs
Create a message about fold change and pvalues used to produce the plot.produce.cutoff.message
Create a warning about pvalue or FDR minimum valueproduce.cutoff.warning
Reformat Ensembl GeneIDsreformat.ensembl
This is data to be included in packagesample_annotation
This is data to be included in packagesample_count_cpm
This is data to be included in packageSample_disease_gene_set
This is data to be included in packageSample_summary_statistics_table
This is data to be included in packageSample_summary_statistics_table1
Second Cutoff ErrorsecondCutoffErr
Transform GeneIDstransform.geneid
Validate Annotation Tablevalidate.annot
Validate Baseline Valuesvalidate.baseline
Check Summary Statistics Required Column Typesvalidate.col.types
Validate Comp Namesvalidate.comp.names
Validate Data Inputvalidate.data
Validate Data in the Context of Annotationvalidate.data.annot
Validate Foldchangevalidate.FC
Validate Flag Value Is Validvalidate.flag
Validate genes presentvalidate.genes.present
Validate Genesetvalidate.geneset
Validate Numeric Columnvalidate.numeric
Validate Pathways DBvalidate.pathways.db
Validate P-value Rangevalidate.pval.range
Validate pval flagvalidate.pvalflag
Validate Pvaluesvalidate.pvals
Validate Single Table is not listvalidate.single.table.isnotlist
Validate Summary Statistics Filevalidate.stats
Check Summary Statistics Required Columnsvalidate.stats.cols
This is data to be included in packagewpA2020