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DESCRIPTION
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Package: psichomics
Title: Graphical Interface for Alternative Splicing Quantification, Analysis and
Visualisation
Version: 1.28.1
Encoding: UTF-8
Authors@R: c(
person("Nuno", "Saraiva-Agostinho",
email="[email protected]", role=c("aut", "cre"),
comment=c(ORCID="0000-0002-5549-105X")),
person(c("Nuno", "Luís"), "Barbosa-Morais", role=c("aut", "led", "ths"),
comment=c(ORCID="0000-0002-1215-0538")),
person("André", "Falcão", role="ths"),
person("Lina", "Gallego Paez", role="ctb"),
person("Marie", "Bordone", role="ctb"),
person("Teresa", "Maia", role="ctb"),
person("Mariana", "Ferreira", role="ctb"),
person("Ana Carolina", "Leote", role="ctb"),
person("Bernardo", "de Almeida", role="ctb"))
Description: 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.
Depends:
R (>= 4.0),
shiny (>= 1.7.0),
shinyBS
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 7.3.1
Imports:
AnnotationDbi,
AnnotationHub,
BiocFileCache,
cluster,
colourpicker,
data.table,
digest,
dplyr,
DT (>= 0.2),
edgeR,
fastICA,
fastmatch,
ggplot2,
ggrepel,
graphics,
grDevices,
highcharter (>= 0.5.0),
htmltools,
httr,
jsonlite,
limma,
pairsD3,
plyr,
purrr,
Rcpp (>= 0.12.14),
recount,
Rfast,
R.utils,
reshape2,
shinyjs,
stringr,
stats,
SummarizedExperiment,
survival,
tools,
utils,
XML,
xtable,
methods
Suggests:
testthat,
knitr,
parallel,
devtools,
rmarkdown,
gplots,
covr,
car,
rstudioapi,
spelling
LinkingTo: Rcpp
VignetteBuilder: knitr
Collate:
'RcppExports.R'
'utils.R'
'globalAccess.R'
'app.R'
'analysis.R'
'analysis_correlation.R'
'analysis_diffExpression.R'
'analysis_diffExpression_event.R'
'analysis_diffExpression_table.R'
'analysis_diffSplicing.R'
'analysis_diffSplicing_event.R'
'analysis_diffSplicing_table.R'
'analysis_dimReduction.R'
'analysis_dimReduction_ica.R'
'analysis_dimReduction_pca.R'
'analysis_information.R'
'analysis_survival.R'
'analysis_template.R'
'data.R'
'formats.R'
'data_firebrowse.R'
'data_geNormalisationFiltering.R'
'data_gtex.R'
'data_inclusionLevels.R'
'data_inclusionLevelsFilter.R'
'data_local.R'
'data_recount.R'
'events_suppa.R'
'events_vastTools.R'
'events_miso.R'
'events_mats.R'
'events.R'
'formats_SraRunTableSampleInfo.R'
'formats_firebrowseGeneExpression.R'
'formats_firebrowseJunctionReads.R'
'formats_firebrowseMergeClinical.R'
'formats_firebrowseNormalizedGeneExpression.R'
'formats_genericClinical.R'
'formats_genericGeneExpression.R'
'formats_genericInclusionLevels.R'
'formats_genericJunctionReads.R'
'formats_genericSampleInfo.R'
'formats_gtexClinical.R'
'formats_gtexGeneReadsFormat.R'
'formats_gtexJunctionReads.R'
'formats_gtexSampleInfo.R'
'formats_gtexV7Clinical.R'
'formats_gtexV7JunctionReads.R'
'formats_gtexV8JunctionReads.R'
'formats_psichomicsGeneExpression.R'
'formats_psichomicsInclusionLevels.R'
'formats_recountSampleInfo.R'
'formats_vasttoolsGeneExpression.R'
'formats_vasttoolsInclusionLevels.R'
'formats_vasttoolsInclusionLevelsTidy.R'
'groups.R'
'help.R'
'utils_drawSplicingEvent.R'
'utils_eventParsing.R'
'utils_fileBrowserDialog.R'
'utils_interactiveGgplot.R'
'utils_interface.R'
biocViews: Sequencing, RNASeq, AlternativeSplicing,
DifferentialSplicing, Transcription, GUI, PrincipalComponent,
Survival, BiomedicalInformatics, Transcriptomics, ImmunoOncology,
Visualization, MultipleComparison, GeneExpression, DifferentialExpression
URL: https://nuno-agostinho.github.io/psichomics/,
https://github.com/nuno-agostinho/psichomics/
BugReports: https://github.com/nuno-agostinho/psichomics/issues
Language: en-GB