Package: psichomics 1.33.0

Nuno Saraiva-Agostinho

psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Authors:Nuno Saraiva-Agostinho [aut, cre], Nuno Luís Barbosa-Morais [aut, led, ths], André Falcão [ths], Lina Gallego Paez [ctb], Marie Bordone [ctb], Teresa Maia [ctb], Mariana Ferreira [ctb], Ana Carolina Leote [ctb], Bernardo de Almeida [ctb]

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psichomics.pdf |psichomics.html✨
psichomics/json (API)
NEWS

# Install 'psichomics' in R:

install.packages('psichomics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nuno-agostinho/psichomics/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:psichomics-1.33.0(bioc 3.21)psichomics-1.32.0(bioc 3.20)

sequencing rnaseq alternativesplicing differentialsplicing transcription gui principalcomponent survival biomedicalinformatics transcriptomics immunooncology visualization multiplecomparison geneexpression differentialexpression alternative-splicing bioconductor data-analyses differential-gene-expression differential-splicing-analysis gene-expression gtex recount2 rna-seq-data splicing-quantification sra tcga vast-tools

7.11 score 35 stars 31 scripts 216 downloads 1 mentions 89 exports 200 dependencies

Last updated 23 days agofrom:55e72bb75b. Checks:OK: 1 NOTE: 4 ERROR: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	NOTE	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	NOTE	Oct 31 2024
R-4.4-mac-x86_64	ERROR	Oct 31 2024
R-4.4-mac-aarch64	ERROR	Oct 31 2024
R-4.3-win-x86_64	NOTE	Oct 31 2024
R-4.3-mac-x86_64	ERROR	Oct 31 2024
R-4.3-mac-aarch64	ERROR	Oct 31 2024

Exports:assignValuePerPatient assignValuePerSubject calculateLoadingsContribution colSums convertGeneIdentifiers correlateGEandAS createGroupByAttribute diffAnalyses discardLowCoveragePSIvalues ensemblToUniprot filterGeneExpr filterGroups filterPSI getAttributesTime getDownloadsFolder getFirebrowseCohorts getFirebrowseDataTypes getFirebrowseDates getGeneList getGenesFromSplicingEvents getGtexDataTypes getGtexReleases getGtexTissues getMatchingSamples getPatientFromSample getSampleFromPatient getSampleFromSubject getSplicingEventData getSplicingEventFromGenes getSplicingEventTypes getSubjectFromSample getTCGAcohorts getTCGAdataTypes getTCGAdates getValuePerPatient getValuePerSubject groupPerElem isFirebrowseUp labelBasedOnCutoff listSplicingAnnotations loadAnnotation loadFirebrowseData loadGtexData loadLocalFiles loadSRAproject loadTCGAdata normaliseGeneExpression normalizeGeneExpression optimalSurvivalCutoff parseCategoricalGroups parseMatsAnnotation parseMisoAnnotation parseSampleGroups parseSplicingEvent parseSuppaAnnotation parseTcgaSampleInfo parseTCGAsampleInfo parseTCGAsampleTypes parseVastToolsAnnotation performICA performPCA plotCorrelation plotDistribution plotGeneExprPerSample plotGroupIndependence plotICA plotLibrarySize plotPCA plotPCAvariance plotProtein plotRowStats plotSplicingEvent plotSurvivalCurves plotSurvivalPvaluesByCutoff plotTranscripts plotVariance prepareAnnotationFromEvents prepareGeneQuant prepareJunctionQuant prepareSRAmetadata processSurvTerms psichomics quantifySplicing queryEnsemblByEvent queryEnsemblByGene readFile survdiffTerms testGroupIndependence testSurvival

Dependencies:abind AnnotationDbi AnnotationHub askpass assertthat backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob broom BSgenome bslib bumphunter cachem checkmate cli clipr cluster codetools colorspace colourpicker commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray derfinder derfinderHelper digest doRNG downloader dplyr DT edgeR evaluate fansi farver fastICA fastmap fastmatch filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges GEOquery ggplot2 ggrepel glue gridExtra gtable highcharter highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme nnet openssl pairsD3 pillar pkgconfig plogr plyr png prettyunits progress promises purrr quantmod qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppGSL RcppParallel RcppZiggurat RCurl readr recount rentrez reshape2 restfulr Rfast Rhtslib rjson rlang rlist rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer rvest S4Arrays S4Vectors sass scales selectr shiny shinyBS shinyjs snow sourcetools SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange tinytex TTR tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable xts XVector yaml zlibbioc zoo

Case study: command-line interface (CLI) tutorial

Nuno Saraiva-Agostinho

Rendered fromCLI_tutorial.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2022-07-14
Started: 2016-09-07

Case study: visual interface tutorial

Nuno Saraiva-Agostinho

Rendered fromGUI_tutorial.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-05-13
Started: 2016-09-07

Loading user-provided data

Nuno Saraiva-Agostinho

Rendered fromcustom_data.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2021-05-27
Started: 2019-03-27

Preparing an Alternative Splicing Annotation for psichomics

Nuno Saraiva Agostinho

Rendered fromAS_events_preparation.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-08-11
Started: 2016-10-08

Help page	Topics
Print startup message	.onAttach
Display results of correlation analyses	as.table.GEandAScorrelation plot.GEandAScorrelation plotCorrelation print.GEandAScorrelation [.GEandAScorrelation
Assign average sample values to their corresponding subjects	assignValuePerPatient assignValuePerSubject getValuePerPatient getValuePerSubject
Calculate the contribution of PCA loadings to the selected principal components	calculateLoadingsContribution
Sum columns using an 'EList-class' object	colSums,EList-method
Convert gene identifiers	convertGeneIdentifiers
Correlate gene expression data against alternative splicing quantification	correlateGEandAS
Split elements into groups based on a given column of a dataset	createGroupByAttribute
Perform statistical analyses	diffAnalyses
Remove alternative splicing quantification values based on coverage	discardLowCoveragePSIvalues
Convert from Ensembl to UniProt identifier	ensemblToUniprot
Filter genes based on their expression	filterGeneExpr
Filter groups with less data points than the threshold	filterGroups
Filter alternative splicing quantification	filterPSI
Get time values for given columns in a clinical dataset	getAttributesTime
Get the path to the Downloads folder	getDownloadsFolder
Get curated, literature-based gene lists	getGeneList
Get GTEx data information	getGtexDataTypes getGtexReleases
Get GTEx tissues from given GTEx sample attributes	getGtexTissues
Get samples matching the given subjects	getMatchingSamples getSampleFromPatient getSampleFromSubject
Get splicing event information for given alternative splicing quantification data	getSplicingEventData
Get alternative splicing events from genes or vice-versa	getGenesFromSplicingEvents getSplicingEventFromGenes
Get supported splicing event types	getSplicingEventTypes
Get subjects from given samples	getPatientFromSample getSubjectFromSample
Get available parameters for TCGA data	getFirebrowseCohorts getFirebrowseDataTypes getFirebrowseDates getTCGAcohorts getTCGAdataTypes getTCGAdates
Assign one group to each element	groupPerElem
Check if FireBrowse API is running	isFirebrowseUp
Label groups based on a given cutoff	labelBasedOnCutoff
List alternative splicing annotations	listSplicingAnnotations
Load alternative splicing annotation from 'AnnotationHub'	loadAnnotation
Download and load GTEx data	loadGtexData
Load local files	loadLocalFiles
Download and load SRA projects via recount2	loadSRAproject
Download and process TCGA data	loadFirebrowseData loadTCGAdata
Filter and normalise gene expression	normaliseGeneExpression normalizeGeneExpression
Calculate optimal data cutoff that best separates survival curves	optimalSurvivalCutoff
Parse categorical columns in a data frame	parseCategoricalGroups
Parse alternative splicing event identifier	parseSplicingEvent
Parse events from alternative splicing annotation	parseMatsAnnotation parseMisoAnnotation parseSuppaAnnotation parseVastToolsAnnotation
Parse sample information from TCGA sample identifiers	parseSampleGroups parseTCGAsampleInfo parseTcgaSampleInfo parseTCGAsampleTypes
Perform independent component analysis after processing missing values	performICA
Perform principal component analysis after processing missing values	performPCA
Plot sample distribution	plotDistribution
Plot distribution of gene expression per sample	plotGeneExprPerSample
Plot '-log10(p-values)' of the results obtained after multiple group independence testing	plotGroupIndependence
Create multiple scatterplots from ICA	plotICA
Plot library size	plotLibrarySize
Create a scatterplot from a PCA object	plotPCA
Create the explained variance plot from a PCA	plotPCAvariance plotVariance
Plot protein features	plotProtein
Plot row-wise statistics	plotRowStats
Plot diagram of alternative splicing events	plotSplicingEvent
Plot survival curves	plotSurvivalCurves
Plot p-values of survival difference between groups based on multiple cutoffs	plotSurvivalPvaluesByCutoff
Plot transcripts	plotTranscripts
Prepare annotation from alternative splicing events	prepareAnnotationFromEvents
Prepare user-provided files to be loaded into psichomics	prepareGeneQuant prepareJunctionQuant prepareSRAmetadata
Process survival curves terms to calculate survival curves	processSurvTerms
Start graphical interface of psichomics	psichomics
Quantify alternative splicing events	quantifySplicing
Query information from Ensembl	queryEnsemblByEvent queryEnsemblByGene
Load psichomics-specific file	readFile
Test Survival Curve Differences	survdiffTerms
Create survival curves	survfit.survTerms
Preserve attributes of 'sticky' objects when extracting or transposing object	t.sticky [.sticky
Multiple independence tests between reference groups and list of groups	testGroupIndependence
Test the survival difference between groups of subjects	testSurvival

Package: psichomics 1.33.0

psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Case study: command-line interface (CLI) tutorial

Case study: visual interface tutorial

Loading user-provided data

Preparing an Alternative Splicing Annotation for psichomics

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)