Package: GenomicSuperSignature 1.15.0

Sehyun Oh

GenomicSuperSignature: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.

Authors:Sehyun Oh [aut, cre], Levi Waldron [aut], Sean Davis [aut]

GenomicSuperSignature_1.15.0.tar.gz
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GenomicSuperSignature.pdf |GenomicSuperSignature.html✨
GenomicSuperSignature/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/shbrief/genomicsupersignature/issues

Datasets:
  • droplist - MeSH terms to be excluded in drawWordcloud function
  • filterList - RAVs that will output with quality-control messages
  • miniAllZ - Subset of allZ matrix constructed from 8 CRC training datasets
  • miniRAVmodel - RAVmodel from 536 studies, annotated with MSigDB C2
  • miniTCGA - Subset of TCGA-COAD and TCGA-BRCA RNA sequencing datasets
  • res_hcut - Subset of allZ matrix constructed from 8 CRC training datasets

On BioConductor:GenomicSuperSignature-1.15.0(bioc 3.21)GenomicSuperSignature-1.14.0(bioc 3.20)

transcriptomicssystemsbiologyprincipalcomponentrnaseqsequencingpathwaysclusteringbioconductor-packageexploratory-data-analysisgseameshprincipal-component-analysisrna-sequencing-profilestransferlearning

6.97 score 16 stars 59 scripts 202 downloads 43 exports 153 dependencies

Last updated 2 months agofrom:675b80731f. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winWARNINGNov 29 2024
R-4.5-linuxWARNINGNov 29 2024
R-4.4-winWARNINGNov 29 2024
R-4.4-macWARNINGNov 29 2024
R-4.3-winWARNINGNov 29 2024
R-4.3-macWARNINGNov 29 2024

Exports:annotatePCannotateRAVavailableRAVmodelbuildAvgLoadingcalculateScoredrawWordcloudextractPCfindKeywordInRAVfindSignaturefindStudiesInClustergeneSetsgeneSets<-getModelgetRAVInfogetStudyInfogseagsea<-heatmapTablemeshmesh<-meshTablePCAGenomicSignaturesPCAsummaryPCAsummary<-PCinRAVplotAnnotatedPCAplotValidateRAVindexrmNaInfsampleScoreHeatmapshowsilhouetteWidthsilhouetteWidth<-studiesstudies<-subsetEnrichedPathwaystrainingDatatrainingData<-updateNoteupdateNote<-validatevalidatedSignaturesversion

Dependencies:abindaskpassbackportsbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbootbroombslibcachemcarcarDatacirclizecliclueclustercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDerivdigestdoBydoParalleldplyrevaluatefansifarverfastmapfilelockflextablefontawesomefontBitstreamVerafontLiberationfontquiverforeachFormulafsgdtoolsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggpubrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehighrhtmltoolshtmlwidgetshttrIRangesirlbaisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivofficeropensslpbkrtestpillarpkgconfigplogrplotlypngpolynompromisespurrrquantregR6raggrappdirsRColorBrewerRcppRcppEigenrjsonrlangrmarkdownRSQLiterstatixS4ArraysS4VectorssassscalesshapeSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviridisLitewithrxfunxml2XVectoryamlzipzlibbioc

Structure and content of RAVmodel

Sehyun Oh

Rendered fromContents.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-09-21
Started: 2022-07-21

GenomicSuperSignature - Quickstart

Sehyun Oh

Rendered fromQuickstart.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-07-26
Started: 2020-07-15

Readme and manuals

Help Manual

Help pageTopics
Annotate top PCs from the datasetannotatePC
Search the top enriched pathways for RAVannotateRAV
List the available RAVmodelsavailableRAVmodel
Calculate average loadings of each clusterbuildAvgLoading
Calculate the validation score for a new datasetcalculateScore
Draw wordcloud using the collection of RAVs' MeSH termsdrawWordcloud
MeSH terms to be excluded in drawWordcloud functiondroplist
PCA on gene expression profileextractPC
RAVs that will output with quality-control messagesfilterList
Find the rank of your keyword in the RAV's GSEA annotationfindKeywordInRAV
Find the RAVs with the keyword-containing enriched pathwaysfindSignature
Find the studies contributing each RAVfindStudiesInCluster
Virtual class inherited from SummarizedExperimentGenomicSignatures-class
Methods and accesors for 'GenomicSignatures' objectcolData geneSets geneSets,GenomicSignatures-method geneSets<- geneSets<-,GenomicSignatures-method GenomicSignatures-methods metadata RAVindex RAVindex,GenomicSignatures-method updateNote updateNote,GenomicSignatures-method updateNote<- updateNote<-,GenomicSignatures-method version,GenomicSignatures-method
Download a PCAGenomicSignatures modelgetModel
Extract information on a specific RAVgetRAVInfo
Extract information on a specific training datasetgetStudyInfo
Validation result in heatmap formatheatmapTable
Build a two-column word/frequency tablemeshTable
Subset of allZ matrix constructed from 8 CRC training datasetsminiAllZ
RAVmodel from 536 studies, annotated with MSigDB C2miniRAVmodel
Subset of TCGA-COAD and TCGA-BRCA RNA sequencing datasetsminiTCGA
Construct 'PCAGenomicSignatures' objectPCAGenomicSignatures
PCAGenomicSignatures-class.PCAGenomicSignatures PCAGenomicSignatures-class
Methods and accesors for 'PCAGenomicSignatures' objectgsea gsea,PCAGenomicSignatures-method gsea<- gsea<-,PCAGenomicSignatures-method mesh mesh,PCAGenomicSignatures-method mesh<- mesh<-,PCAGenomicSignatures-method PCAGenomicSignatures-methods PCAsummary PCAsummary,PCAGenomicSignatures-method PCAsummary<- PCAsummary<-,PCAGenomicSignatures-method show,PCAGenomicSignatures-method silhouetteWidth silhouetteWidth,PCAGenomicSignatures-method silhouetteWidth<- silhouetteWidth<-,PCAGenomicSignatures-method studies studies,PCAGenomicSignatures-method studies<- studies<-,PCAGenomicSignatures-method trainingData trainingData,PCAGenomicSignatures-method trainingData<- trainingData<-,PCAGenomicSignatures-method
Extract the list of PCs in a clusterPCinRAV
Two-dimensional PCA plot with the PC annotationplotAnnotatedPCA
Plot validation results in an interactive graphplotValidate
Subset of allZ matrix constructed from 8 CRC training datasetsres_hcut
Remove rows with missing and Inf values from a matrixrmNaInf
Plot heatmap of the sample scoressampleScoreHeatmap
Subset enriched pathways of RAVsubsetEnrichedPathways
Validate new datasetsvalidate
Validation result in data framevalidatedSignatures