Package: curatedPCaData 1.9.0

Teemu Daniel Laajala

curatedPCaData: Curated Prostate Cancer Data

The package curatedPCaData offers a selection of annotated prostate cancer datasets featuring multiple omics, manually curated metadata, and derived downstream variables. The studies are offered as MultiAssayExperiment (MAE) objects via ExperimentHub, and comprise of clinical characteristics tied to gene expression, copy number alteration and somatic mutation data. Further, downstream features computed from these multi-omics data are offered. Multiple vignettes help grasp characteristics of the various studies and provide example exploratory and meta-analysis of leveraging the multiple studies provided here-in.

Authors:Teemu Daniel Laajala [aut, cre], Jordan Creed [ctb], Christelle Colin Leitzinger [ctb], Varsha Sreekanth [ctb], Federico Calboli [ctb], Kalaimathy Singaravelu [ctb], Michael Orman [ctb], Alex Soupir [ctb], Anni Halkola [ctb]

curatedPCaData_1.9.0.tar.gz
curatedPCaData_1.9.0.tar.gz(r-4.7-any)curatedPCaData_1.9.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedPCaData/json (API)

# Install 'curatedPCaData' in R:

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

Bug tracker:https://github.com/syksy/curatedpcadata/issues

Datasets:

template_prad - Template for curatedPCaData clinical fields

On BioConductor:curatedPCaData-1.9.0(data/experiment 3.24)curatedPCaData-1.8.0(data/experiment 3.23)

experimenthub experimentdata prostatecancerdata cancerdata homo_sapiens_data microarraydata rnaseqdata expressiondata copynumbervariationdata somatic geo reproducibleresearch cancer cancer-data cancer-genomics cancer-research datapkg

5.82 score 11 stars 12 scripts 6 exports 72 dependencies

Last updated from:6316670fff. Checks:3 NOTE, 1 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	NOTE	204
linux-devel	NOTE	926
source / vignettes	OK	579
linux-release	NOTE	878

Exports:getPCa getPCaStudies getPCaSummarySamples getPCaSummaryStudies getPCaSummarySurv getPCaSummaryTable

Dependencies:abind AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr DelayedArray dplyr ExperimentHub fastmap filelock generics GenomicRanges glue httr httr2 IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment openssl pillar pkgconfig plyr png purrr R6 RaggedExperiment rappdirs Rcpp reshape2 rlang RSQLite S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

Overview to curatedPCaData

Rendered fromoverview.Rmdusingknitr::rmarkdown

Last update: 2023-11-02
Started: 2022-02-10

Help page	Topics
Abida et al. MAE-object	curatedPCaDatasets_abida
Baca et al. MAE-object	curatedPCaDatasets_baca
Barbieri et al. MAE-object	curatedPCaDatasets_barbieri
Barwick et al. MAE-object	curatedPCaDatasets_barwick
Chandran et al., Yu et al. MAE-object	curatedPCaDatasets_chandran
Friedrich et al. MAE-object	curatedPCaDatasets_friedrich
Hieronymus et al. MAE-object	curatedPCaDatasets_hieronymus
ICGC CA MAE-object	curatedPCaDatasets_icgcca
International Genomics Consortium (IGC) MAE-object	curatedPCaDatasets_igc
Kim et al. MAE-object	curatedPCaDatasets_kim
Kunderfranco et al. MAE-object	curatedPCaDatasets_kunderfranco
Ren et al. MAE-object	curatedPCaDatasets_ren
Sun et al. MAE-object	curatedPCaDatasets_sun
Taylor et al. MAE-object	curatedPCaDatasets_taylor
TCGA MAE-object	curatedPCaDatasets_tcga
True et al. MAE-object	curatedPCaDatasets_true
Wallace et al. MAE-object	curatedPCaDatasets_wallace
Wang et al. MAE-object	curatedPCaDatasets_wang
Weiner et al. MAE-object	curatedPCaDatasets_weiner
Construct Prostate Cancer MultiAssayExperiment object from specific cohort	getPCa
Create a vector of unique study identifiers available in curatedPCaData	getPCaStudies
Create a summary table for sample counts for different omics across the datasets in curatedPCaData	getPCaSummarySamples
Create a summary table of key characteristics for each study	getPCaSummaryStudies
Create survival summary for metadata in curatedPCaData	getPCaSummarySurv
Create summary tables for colData metadata in curatedPCaData	getPCaSummaryTable
Template for curatedPCaData clinical fields	template_prad

Package: curatedPCaData 1.9.0

curatedPCaData: Curated Prostate Cancer Data

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Help Manual

Usage by other packages (reverse dependencies)