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CTexploreR

This is the development version of CTexploreR; to use it, please install the devel version of Bioconductor.

Explores Cancer Testis Genes


Bioconductor version: Development (3.19)

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

Author: Axelle Loriot [aut, cre] , Julie Devis [aut] , Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths]

Maintainer: Axelle Loriot <axelle.loriot at uclouvain.be>

Citation (from within R, enter citation("CTexploreR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CTexploreR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews DNAMethylation, DataImport, DifferentialExpression, Epigenetics, ExperimentHubSoftware, GeneExpression, Software, Transcriptomics
Version 0.99.5
In Bioconductor since BioC 3.19 (R-4.4)
License Artistic-2.0
Depends R (>= 4.3), CTdata
Imports BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment, GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang, grDevices, stats, circlize, ggrepel, SingleCellExperiment, MatrixGenerics
System Requirements
URL https://github.com/UCLouvain-CBIO/CTexploreR
Bug Reports https://github.com/UCLouvain-CBIO/CTexploreR/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CTexploreR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CTexploreR
Package Short Url https://bioconductor.org/packages/CTexploreR/
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