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_pkgdown.yml
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url: https://nuno-agostinho.github.io/psichomics/
home:
title: Visual interface for alternative splicing analysis and visualisation
destination: docs
reference:
- title: "General functions"
contents:
- psichomics
- parseSplicingEvent
- getSplicingEventData
- getSplicingEventFromGenes
- getGenesFromSplicingEvents
- plotSplicingEvent
- parseCategoricalGroups
- getDownloadsFolder
- title: "TCGA data retrieval"
desc: >
Retrieve TCGA data using
[Firebrowse API](http://firebrowse.org/api-docs/)
contents:
- isFirebrowseUp
- getTCGAcohorts
- getTCGAdataTypes
- getTCGAdates
- loadTCGAdata
- parseTCGAsampleInfo
- title: "GTEx data retrieval"
contents:
- getGtexReleases
- getGtexDataTypes
- getGtexTissues
- loadGtexData
- title: "SRA data retrieval"
contents:
- loadSRAproject
- title: "User-provided data loading"
contents:
- loadLocalFiles
- prepareJunctionQuant
- prepareGeneQuant
- title: "Gene expression pre-processing"
contents:
- plotRowStats
- plotGeneExprPerSample
- plotLibrarySize
- filterGeneExpr
- normaliseGeneExpression
- convertGeneIdentifiers
- title: "PSI quantification and filtering"
contents:
- getSplicingEventTypes
- listSplicingAnnotations
- loadAnnotation
- quantifySplicing
- discardLowCoveragePSIvalues
- filterPSI
- plotRowStats
- title: "Custom alternative splicing annotation"
contents:
- parseMatsAnnotation
- parseMisoAnnotation
- parseSuppaAnnotation
- parseVastToolsAnnotation
- prepareAnnotationFromEvents
- title: "Data Grouping"
contents:
- createGroupByAttribute
- filterGroups
- groupPerElem
- getGeneList
- getSampleFromSubject
- getSubjectFromSample
- testGroupIndependence
- plotGroupIndependence
- title: "Principal component analysis (PCA)"
contents:
- performPCA
- plotPCAvariance
- calculateLoadingsContribution
- plotPCA
- title: "Independent component analysis (ICA)"
contents:
- performICA
- plotICA
- title: "Differential analyses"
contents:
- diffAnalyses
- plotDistribution
- title: "Gene expression and alternative splicing correlation"
contents:
- correlateGEandAS
- plotCorrelation
- title: "Survival analysis"
contents:
- getAttributesTime
- processSurvTerms
- survfit.survTerms
- survdiffTerms
- plotSurvivalCurves
- testSurvival
- assignValuePerSubject
- labelBasedOnCutoff
- optimalSurvivalCutoff
- plotSurvivalPvaluesByCutoff
- title: "Gene, transcript and protein annotation retrieval"
contents:
- queryEnsemblByEvent
- queryEnsemblByGene
- ensemblToUniprot
- plotProtein
- plotTranscripts
- title: internal
contents:
- colSums,EList-method
- .onAttach
- readFile
- t.sticky
articles:
- title: All vignettes
contents:
- GUI_tutorial
- CLI_tutorial
- custom_data
- AS_events_preparation
navbar:
components:
articles:
text: Tutorials
menu:
- text: 'Visual interface tutorial'
href: articles/GUI_tutorial.html
- text: 'Command-line interface (CLI) tutorial'
href: articles/CLI_tutorial.html
- text: 'Loading user-provided data'
href: articles/custom_data.html
- text: 'Preparing custom alternative splicing annotations'
href: articles/AS_events_preparation.html
template:
bootstrap: 5
params:
ganalytics: UA-156449666-1
docsearch:
api_key: fa0226bf1a3df7e1c8ab8f0e70450e0a
index_name: stem-cell-analysis-in-psichomics
news:
- one_page: false