CTexploreR

This is the development version of CTexploreR; for the stable release version, see CTexploreR.

Explores Cancer Testis Genes

Bioconductor version: Development (3.21)

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] (ORCID: ), Julie Devis [aut] (ORCID: ), Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CTexploreR")

Cancer Testis Explorer	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DataImport, DifferentialExpression, Epigenetics, ExperimentHubSoftware, GeneExpression, Software, Transcriptomics
Version	1.1.2
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
License	Artistic-2.0
Depends	R (>= 4.3), CTdata(>= 1.5.3)
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

Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), InteractiveComplexHeatmap
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	CTexploreR_1.1.2.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/CTexploreR/
Package Short Url	https://bioconductor.org/packages/CTexploreR/
Package Downloads Report	Download Stats