Package: bulkAnalyseR 1.1.0

Ilias Moutsopoulos

bulkAnalyseR: Interactive Shiny App for Bulk Sequencing Data

Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.

Authors:Ilias Moutsopoulos [aut, cre], Eleanor Williams [aut, ctb], Irina Mohorianu [aut, ctb]

bulkAnalyseR_1.1.0.tar.gz
bulkAnalyseR_1.1.0.zip(r-4.5)bulkAnalyseR_1.1.0.zip(r-4.4)bulkAnalyseR_1.1.0.zip(r-4.3)
bulkAnalyseR_1.1.0.tgz(r-4.4-any)bulkAnalyseR_1.1.0.tgz(r-4.3-any)
bulkAnalyseR_1.1.0.tar.gz(r-4.5-noble)bulkAnalyseR_1.1.0.tar.gz(r-4.4-noble)
bulkAnalyseR_1.1.0.tgz(r-4.4-emscripten)bulkAnalyseR_1.1.0.tgz(r-4.3-emscripten)
bulkAnalyseR.pdf |bulkAnalyseR.html✨
bulkAnalyseR/json (API)

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

Peer review:

Bug tracker:https://github.com/core-bioinformatics/bulkanalyser/issues

On CRAN:

59 exports 25 stars 2.36 score 166 dependencies 13 scripts 346 downloads

Last updated 10 months agofrom:b4b069328e. Checks:ERROR: 4 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesFAILSep 10 2024
R-4.5-winWARNINGSep 10 2024
R-4.5-linuxERRORSep 10 2024
R-4.4-winWARNINGSep 10 2024
R-4.4-macWARNINGSep 10 2024
R-4.3-winERRORSep 10 2024
R-4.3-macERRORSep 10 2024

Exports:%>%calculate_condition_mean_sd_per_genecross_plotcrossPanelServercrossPanelUIDEanalysis_deseq2DEanalysis_edgerDEpanelServerDEpanelUIDEplotPanelServerDEplotPanelUIDEsummaryPanelServerDEsummaryPanelUIdetermine_udsenrichmentPanelServerenrichmentPanelUIexpression_heatmapfind_regulators_with_recurring_edgesgenerateShinyAppgenes_barplotget_link_list_renameGRNCisPanelServerGRNCisPanelUIGRNCustomPanelServerGRNCustomPanelUIGRNpanelServerGRNpanelUIGRNTransPanelServerGRNTransPanelUIinfer_GRNjaccard_heatmapjaccard_indexlandingPanelServerlandingPanelUIma_enhancema_plotmake_heatmap_matrixmake_pattern_matrixmodalityPanelServermodalityPanelUInoisyr_counts_with_plotpatternPanelServerpatternPanelUIplot_GRNplot_line_patternplot_pcaplot_upsetpreprocess_miRTarBasepreprocessExpressionMatrixqc_density_plotqc_violin_plotQCpanelServerQCpanelUIrescale_matrixsampleSelectPanelServersampleSelectPanelUIscatter_plotvolcano_enhancevolcano_plot

Dependencies:abindadmiscanytimeaplotaskpassbase64encbeeswarmBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemCairocirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcpp11crayoncrosstalkcurldata.tableDelayedArrayDESeq2digestdoParalleldplyrDTedgeRevaluatefansifarverfastmapfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsgenericsGENIE3GenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggforceggfunggnewscaleggplot2ggplotifyggrastrggrepelggVennDiagramGlobalOptionsgluegprofiler2gridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmenoisyropensslpatchworkphilentropypillarpkgconfigplotlyplyrpngpolyclippoormanpreprocessCorepromisespurrrR6raggrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2RhtslibrjsonrlangrmarkdownRsamtoolsS4ArraysS4VectorssassscalesshapeshinyshinyjquishinyjsshinyLPshinyWidgetssnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttinytextweenrUCSC.utilsUpSetRutf8vctrsvennviporviridisLitevisNetworkwithrxfunxtableXVectoryamlyulab.utilszlibbioc

Readme and manuals

Help Manual

Help pageTopics
Calculate statistics for each gene of an expression matrix given a groupingcalculate_condition_mean_sd_per_gene
Create a cross plot comparing differential expression (DE) resultscross_plot
Generate the cross plot panel of the shiny appcrossPanel crossPanelServer crossPanelUI
Perform differential expression (DE) analysis on an expression matrixDEanalysis DEanalysis_deseq2 DEanalysis_edger
Generate the DE panel of the shiny appDEpanel DEpanelServer DEpanelUI
Generate the DE plot plot panel of the shiny appDEplotPanel DEplotPanelServer DEplotPanelUI
Generate the DE summary panel of the shiny appDEsummaryPanel DEsummaryPanelServer DEsummaryPanelUI
Determine the pattern between two intervalsdetermine_uds
Generate the enrichment panel of the shiny appenrichmentPanel enrichmentPanelServer enrichmentPanelUI
Create heatmap of an expression matrixexpression_heatmap
Find recurring regulatorsfind_regulators_with_recurring_edges
Generate all files required for an autonomous shiny appgenerateShinyApp
Create a bar plot of expression for selected genes across samples in an experimentgenes_barplot
Convert the adjacency matrix to network linksget_link_list_rename
Generate the GRN cis integration panel of the shiny appGRNCisPanel GRNCisPanelServer GRNCisPanelUI
Generate the GRN custom integration panel of the shiny appGRNCustomPanel GRNCustomPanelServer GRNCustomPanelUI
Generate the GRN panel of the shiny appGRNpanel GRNpanelServer GRNpanelUI
Generate the GRN trans integration panel of the shiny appGRNTransPanel GRNTransPanelServer GRNTransPanelUI
Perform GRN inferenceinfer_GRN
Create a heatmap of the Jaccard similarity index (JSI) between samples of an experimentjaccard_heatmap
Calculate the Jaccard similarity index (JSI) between two vectorsjaccard_index
Generate the landing page panel of the shiny applandingPanel landingPanelServer landingPanelUI
Create an MA plot visualising differential expression (DE) resultsma_enhance ma_plot
Create a matrix of the average expression of each gene in each conditionmake_heatmap_matrix
Create a matrix of the patterns between conditionsmake_pattern_matrix
Generate an app panel for a modalitymodalityPanel modalityPanelServer modalityPanelUI
Apply a modified noisyR counts pipeline printing a plotnoisyr_counts_with_plot
Generate the expression patterns panel of the shiny apppatternPanel patternPanelServer patternPanelUI
Plot a GRNplot_GRN
Create a line plot of average expression across conditionsplot_line_pattern
Create a principal component analysis (PCA) plot the samples of an experimentplot_pca
Visualise the overlap of edges between different networksplot_upset
Creates a comparison table for miRTarBase to be used for custom integrationpreprocess_miRTarBase
Pre-process the expression matrix before generating the shiny apppreprocessExpressionMatrix
Create a density plot of log2 expression across samples of an experimentqc_density_plot
Create a violin/box plot of expression across samples of an experimentqc_violin_plot
Generate the QC panel of the shiny appQCpanel QCpanelServer QCpanelUI
Rescale a matrixrescale_matrix
Generate the sample select panel of the shiny appsampleSelectPanel sampleSelectPanelServer sampleSelectPanelUI
Create a scatter plot of expression between two samples of an experimentscatter_plot
Create a volcano plot visualising differential expression (DE) resultsvolcano_enhance volcano_plot