Package: teal.modules.hermes 0.1.6.9020

Daniel Sabanés Bové

teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application

RNA-seq analysis teal modules based on the `hermes` package.

Authors:Daniel Sabanés Bové [aut, cre], Nikolas Burkoff [aut], Dinakar Kulkarni [aut], Konrad Pagacz [aut], Namrata Bhatia [aut], Dawid Kaledkowski [aut], Pawel Rucki [aut], Jeff Luong [aut], Stefanie Bienert [aut], Haocheng Li [aut], Lyndsee Midori Zhang [aut], Sorin Voicu [ctb], Benoit Falquet [ctb], Mahmoud Hallal [ctb], Tim Treis [ctb], Vedha Viyash [ctb], F. Hoffmann-La Roche AG [cph, fnd]

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teal.modules.hermes.pdf |teal.modules.hermes.html✨
teal.modules.hermes/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/insightsengineering/teal.modules.hermes/issues

Datasets:

    On CRAN:

    modulesrna-seq-analysisshiny

    65 exports 7 stars 3.19 score 215 dependencies 32 scripts

    Last updated 10 days agofrom:1dc4bbb3dd. Checks:OK: 2 NOTE: 4 ERROR: 1. Indexed: no.

    TargetResultDate
    Doc / VignettesOKAug 29 2024
    R-4.5-winNOTEAug 29 2024
    R-4.5-linuxNOTEAug 29 2024
    R-4.4-winNOTEAug 29 2024
    R-4.4-macNOTEAug 29 2024
    R-4.3-winOKJul 25 2024
    R-4.3-macERRORAug 29 2024

    Exports:adtteSpecInputadtteSpecServerassaySpecInputassaySpecServerassert_adtte_varsassert_reactiveassert_summary_funsassert_tagcheck_reactivecheck_tagexpect_tagexperimentSpecInputexperimentSpecServergeneSpecInputgeneSpecServerh_assign_to_group_listh_collapse_levelsh_extract_wordsh_gene_datah_km_mae_to_adtteh_order_genesh_parse_genesh_update_gene_selectionheatmap_plotis_blankmultiSampleVarSpecServersample_tm_g_barplotsample_tm_g_boxplotsample_tm_g_forest_ttesample_tm_g_kmsample_tm_g_pcasample_tm_g_qualitysample_tm_g_scatterplotsample_tm_g_volcanoplotsampleVarSpecInputsampleVarSpecServersrv_g_barplotsrv_g_boxplotsrv_g_forest_ttesrv_g_kmsrv_g_pcasrv_g_qualitysrv_g_scatterplotsrv_g_volcanoplottest_reactivetest_tagtm_g_barplottm_g_boxplottm_g_forest_ttetm_g_kmtm_g_pcatm_g_qualitytm_g_scatterplottm_g_volcanoplottop_gene_plotui_g_barplotui_g_boxplotui_g_forest_tteui_g_kmui_g_pcaui_g_qualityui_g_scatterplotui_g_volcanoplotvalidate_gene_specvalidate_n_levels

    Dependencies:abindAnnotationDbianytimeaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64blobbootbroombslibcachemcarcarDatacheckmatecirclizecliclueclustercodetoolscolorspacecommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDerivDESeq2digestdoBydoParalleldplyrDTedgeRemmeansEnvStatsestimabilityevaluatefansifarverfastmapfilelockflextablefontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachformatRformattersfsfutile.loggerfutile.optionsfuturegdtoolsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggfortifyggplot2ggrepelGlobalOptionsglobalsgluegridExtragtablehermeshighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistenvlme4locfitloggermagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMultiAssayExperimentmunsellmvtnormnlmenloptrnnetnortestnumDerivofficeropensslparallellypbkrtestpillarpkgconfigplogrplotlypngprettyunitsprogresspromisespurrrquantregR.cacheR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackrenvrjsonrlangrlistingsrmarkdownrprojrootRSQLitertablesS4ArraysS4VectorssassscalesshapeshinyshinybusyshinycssloadersshinyjsshinyRadioMatrixshinyWidgetssnowsourcetoolsSparseArraySparseMstatmodstringistringrstylerSummarizedExperimentsurvivalsyssystemfontstealteal.codeteal.datateal.loggerteal.reporterteal.sliceteal.widgetsterntextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviridisLitewithrxfunxml2xtableXVectoryamlzipzlibbioc

    Getting Started

    Rendered fromGetting_Started.Rmdusingknitr::rmarkdownon Aug 29 2024.

    Last update: 2024-03-15
    Started: 2023-01-24

    Readme and manuals

    Help Manual

    Help pageTopics
    'teal.modules.hermes' Packageteal.modules.hermes-package teal.modules.hermes
    Module Input for 'ADTTE' SpecificationadtteSpecInput
    Module Server for 'ADTTE' SpecificationadtteSpecServer
    Module Input for Assay SpecificationassaySpecInput
    Module Server for Assay SpecificationassaySpecServer
    Check for 'ADTTE' Variablesassert_adtte_vars
    Check for List of Summary Functionsassert_summary_funs
    Check for Reactive Inputassert_reactive check_reactive test_reactive
    Check for Shiny Tagassert_tag check_tag expect_tag test_tag
    Module Input for Experiment SpecificationexperimentSpecInput
    Module Server for Experiment SpecificationexperimentSpecServer
    Module Input for Gene Signature SpecificationgeneSpecInput
    Module Server for Gene Signature SpecificationgeneSpecServer
    Helper Function For Group List Creationh_assign_to_group_list
    Helper Function for Collapsing of Factor Levelsh_collapse_levels
    Helper Function to Extract Wordsh_extract_words
    Helper Function to Format Gene Choicesh_gene_data
    Data Preprocessing for 'ADTTE' Moduleh_km_mae_to_adtte
    Helper Function to Order Gene Choicesh_order_genes
    Helper Function to Parse Genesh_parse_genes
    Helper Function to Update Gene Selectionh_update_gene_selection
    Correlation Heatmap Plotheatmap_plot
    Checking for Empty Stringis_blank
    Module Server for Specification of Multiple Sample VariablesmultiSampleVarSpecServer
    Module Input for Sample Variable SpecificationsampleVarSpecInput
    Module Server for Sample Variable SpecificationsampleVarSpecServer
    Teal Module for RNA-seq Barplotsample_tm_g_barplot srv_g_barplot tm_g_barplot ui_g_barplot
    Teal Module for RNA-seq Boxplotsample_tm_g_boxplot srv_g_boxplot tm_g_boxplot ui_g_boxplot
    Teal Module for Survival Forest Plotsample_tm_g_forest_tte srv_g_forest_tte tm_g_forest_tte ui_g_forest_tte
    Teal Module for 'Kaplan-Meier' Plotsample_tm_g_km srv_g_km tm_g_km ui_g_km
    Teal Module for PCA Analysissample_tm_g_pca srv_g_pca tm_g_pca ui_g_pca
    Teal Module for RNA-seq Quality Controlsample_tm_g_quality srv_g_quality tm_g_quality ui_g_quality
    Teal Module for RNA-seq Scatterplotsample_tm_g_scatterplot srv_g_scatterplot tm_g_scatterplot ui_g_scatterplot
    Teal Module for RNA-seq Volcano Plotsample_tm_g_volcanoplot srv_g_volcanoplot tm_g_volcanoplot ui_g_volcanoplot
    Most Expressed Genes Plottop_gene_plot
    Validation of Gene Specificationvalidate_gene_spec
    Validation of Number of Levelsvalidate_n_levels