Package: cbaf 1.35.0

Arman Shahrisa

cbaf: Automated functions for comparing various omic data from cbioportal.org

This package contains functions that allow analysing and comparing omic data across various cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.

Authors:Arman Shahrisa [aut, cre, cph], Maryam Tahmasebi Birgani [aut]

cbaf_1.35.0.tar.gz
cbaf_1.35.0.zip(r-4.7)cbaf_1.35.0.zip(r-4.6)cbaf_1.35.0.zip(r-4.5)
cbaf_1.35.0.tgz(r-4.6-any)cbaf_1.35.0.tgz(r-4.5-any)
cbaf_1.35.0.tar.gz(r-4.7-any)cbaf_1.35.0.tar.gz(r-4.6-any)
cbaf_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cbaf/json (API)

# Install 'cbaf' in R:

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

On BioConductor:cbaf-1.35.0(bioc 3.24)cbaf-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

software assaydomain dnamethylation geneexpression transcription microarray researchfield biomedicalinformatics comparativegenomics epigenetics genetics transcriptomics

3.48 score 2 scripts 345 downloads 9 exports 146 dependencies

Last updated from:cb59d464b4. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	203
linux-devel-x86_64	OK	454
source / vignettes	OK	309
linux-release-x86_64	OK	424
macos-release-arm64	OK	287
macos-oldrel-arm64	OK	346
windows-devel	OK	364
windows-release	OK	404
windows-oldrel	OK	341
wasm-release	OK	184

Exports:automatedStatistics availableData cleanDatabase heatmapOutput obtainMultipleStudies obtainOneStudy processMultipleStudies processOneStudy xlsxOutput

Dependencies:abind annotate AnnotationDbi AnVIL AnVILBase askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem caTools cBioPortalData cigarillo cli clipr codetools commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr DT evaluate fastmap filelock fontawesome formatR fs futile.logger futile.options GCPtools genefilter generics GenomeInfoDb GenomicAlignments GenomicDataCommons GenomicFeatures GenomicRanges glue gplots gtools highr hms htmltools htmlwidgets httpuv httr httr2 IRanges jquerylib jsonlite KEGGREST KernSmooth keyring knitr lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime miniUI MultiAssayExperiment openssl openxlsx otel pillar pkgconfig png prettyunits progress promises purrr R6 RaggedExperiment rapiclient rappdirs RColorBrewer Rcpp RCurl readr restfulr Rhtslib rjson RJSONIO rlang rmarkdown Rsamtools RSQLite RTCGAToolbox rtracklayer rvest S4Arrays S4Vectors sass selectr Seqinfo shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment survival sys TCGAutils tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs vroom withr xfun XML xml2 xtable XVector yaml zip

cbaf: an automated, easy-to-use R package for comparing omic data across multiple cancers / a cancer's subgroups

Rendered fromcbaf.Rmdusingknitr::rmarkdown

Last update: 2024-06-02
Started: 2017-08-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Perform the requested statistics for various studies / subgroups of a study.	automatedStatistics
Check which Data types are available for each cancer study.	availableData
Clean the created database(s)	cleanDatabase
Generate heatmaps for various studies/subgroups of a study.	heatmapOutput
Obtain the requested data for various cancer studies.	obtainMultipleStudies
Obtain the requested data for various subgroups of a cancer study.	obtainOneStudy
Check Expression/methylation Profile for various cancer studies.	processMultipleStudies
Check Expression/methylation Profile for various subgroups of a cancer study.	processOneStudy
Generate excel output for various studies/subgroups of a study.	xlsxOutput