| Title: | ExperimentHub data for the cfTools package |
|---|---|
| Description: | 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] (ORCID: <https://orcid.org/0000-0002-0563-8957>), Shuo Li [aut] (ORCID: <https://orcid.org/0000-0002-1960-6016>), Xianghong Jasmine Zhou [aut] (ORCID: <https://orcid.org/0000-0002-4522-7490>), Wenyuan Li [aut] (ORCID: <https://orcid.org/0000-0002-5029-8525>) |
| Maintainer: | Ran Hu <[email protected]> |
| License: | file LICENSE |
| Version: | 1.10.0 |
| Built: | 2026-10-10 11:16:42 UTC |
| Source: | https://github.com/bioc/cfToolsData |
The cfToolsData package supplies 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 cancer types and 29 primary human tissue types as example files for the CancerDetector and the cfDeconvolve function.
For more information, see https://doi.org/10.1038/s41467-022-32995-6 and https://doi.org/10.1073/pnas.2305236120.
Downloads and caches '.txt.gz' or HDF5-formatted '.h5' files.
Ran Hu
The shape parameters of beta distribution characterizing methylation markers associated with colon adenocarcinoma (COAD)
Downloads and caches a '.txt.gz' file.
COADMarkerParams <- COAD.tumorMarkerParams.hg19() COADMarkerParamsCOADMarkerParams <- COAD.tumorMarkerParams.hg19() COADMarkerParams
The 1st deep neural network in cfSort.
Downloads and caches a '.h5' file in HDF5 format.
modelDNN1 <- DNN1() modelDNN1modelDNN1 <- DNN1() modelDNN1
The 2nd deep neural network in cfSort.
Downloads and caches a '.h5' file in HDF5 format.
modelDNN2 <- DNN2() modelDNN2modelDNN2 <- DNN2() modelDNN2
The shape parameters of beta distribution characterizing methylation markers associated with liver hepatocellular carcinoma (LIHC)
Downloads and caches a '.txt.gz' file.
LIHCMarkerParams <- LIHC.tumorMarkerParams.hg19() LIHCMarkerParamsLIHCMarkerParams <- LIHC.tumorMarkerParams.hg19() LIHCMarkerParams
The shape parameters of beta distribution characterizing methylation markers associated with lung cancer
Downloads and caches a '.txt.gz' file.
LUNGMarkerParams <- LUNG.tumorMarkerParams.hg19() LUNGMarkerParamsLUNGMarkerParams <- LUNG.tumorMarkerParams.hg19() LUNGMarkerParams
The shape parameters of beta distribution characterizing methylation markers associated with stomach adenocarcinoma (STAD)
Downloads and caches a '.txt.gz' file.
STADMarkerParams <- STAD.tumorMarkerParams.hg19() STADMarkerParamsSTADMarkerParams <- STAD.tumorMarkerParams.hg19() STADMarkerParams
The annotation of strategies used to identify tissue markers.
Downloads and caches a '.txt.gz' file.
tissueMarkerAnnot <- tissueMarkerParams.annot() tissueMarkerAnnottissueMarkerAnnot <- tissueMarkerParams.annot() tissueMarkerAnnot
The shape parameters of beta distribution characterizing methylation markers specific to 29 primary human tissue types
Downloads and caches a '.txt.gz' file.
tissueMarkerParams <- tissueMarkerParams.hg19() tissueMarkerParamstissueMarkerParams <- tissueMarkerParams.hg19() tissueMarkerParams