Package: cfToolsData 1.10.0

Ran Hu

cfToolsData: ExperimentHub data for the cfTools package

The cfToolsData package supplies the data for the cfTools package. It contains two pre-trained deep neural network (DNN) models for the cfSort function. Additionally, it includes the shape parameters of beta distribution characterizing methylation markers associated with four tumor types for the CancerDetector function, as well as the parameters characterizing methylation markers specific to 29 primary human tissue types for the cfDeconvolve function.

Authors:Ran Hu [aut, cre], Shuo Li [aut], Xianghong Jasmine Zhou [aut], Wenyuan Li [aut]

cfToolsData_1.10.0.tar.gz
cfToolsData_1.10.0.tar.gz(r-4.7-any)cfToolsData_1.10.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cfToolsData/json (API)

# Install 'cfToolsData' in R:

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

Bug tracker:https://github.com/jasminezhoulab/cftoolsdata/issues

On BioConductor:cfToolsData-1.11.0(data/experiment 3.24)cfToolsData-1.10.0(data/experiment 3.23)

experimenthub experimentdata reproducibleresearch diseasemodel cancerdata tissue datapkg

4.78 score 1 stars 1 packages 2 scripts 8 exports 57 dependencies

Last updated from:63b2d81435 (on RELEASE_3_23). Checks:1 NOTE, 3 OK. Indexed: no.

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

Target	Result	Time
bioc-checks	NOTE	248
linux-devel	OK	278
source / vignettes	OK	207
linux-release	OK	324

Exports:COAD.tumorMarkerParams.hg19 DNN1 DNN2 LIHC.tumorMarkerParams.hg19 LUNG.tumorMarkerParams.hg19 STAD.tumorMarkerParams.hg19 tissueMarkerParams.annot tissueMarkerParams.hg19

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fastmap filelock generics glue httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig png purrr R6 rappdirs rlang RSQLite S4Vectors Seqinfo stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

cfToolsData package

Session information

Rendered fromcfToolsData.Rmdusingknitr::rmarkdown

Last update: 2023-10-05
Started: 2023-09-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ExperimentHub datasets for the cfTools package	cfToolsData
Parameters of COAD markers	COAD.tumorMarkerParams.hg19
Model DNN1	DNN1
Model DNN2	DNN2
Parameters of LIHC markers	LIHC.tumorMarkerParams.hg19
Parameters of lung cancer markers	LUNG.tumorMarkerParams.hg19
Parameters of STAD markers	STAD.tumorMarkerParams.hg19
Annotation of tissue markers	tissueMarkerParams.annot
Parameters of tissue markers	tissueMarkerParams.hg19