Package: CTexploreR 1.1.0

Axelle Loriot

CTexploreR: Explores Cancer Testis Genes

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.

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

CTexploreR_1.1.0.tar.gz
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CTexploreR.pdf |CTexploreR.html✨
CTexploreR/json (API)
NEWS

# Install 'CTexploreR' in R:

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

Bug tracker:https://github.com/uclouvain-cbio/ctexplorer/issues

On BioConductor:CTexploreR-1.1.0(bioc 3.20)CTexploreR-1.0.0(bioc 3.19)

bioconductor-package

12 exports 1.31 score 100 dependencies

Last updated 2 months agofrom:da2dcf314d

Exports:CCLE_expression CT_correlated_genes CT_genes DAC_induction GTEX_expression HPA_cell_type_expression normal_tissue_expression_multimapping normal_tissues_mean_methylation normal_tissues_methylation TCGA_expression TCGA_methylation_expression_correlation testis_expression

Dependencies:abind AnnotationDbi AnnotationHub askpass Biobase BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon CTdata curl DBI dbplyr DelayedArray digest doParallel dplyr ExperimentHub fansi farver fastmap filelock foreach generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggplot2 ggrepel GlobalOptions glue gtable httr IRanges isoband iterators jsonlite KEGGREST labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png purrr R6 rappdirs RColorBrewer Rcpp rjson rlang RSQLite S4Arrays S4Vectors scales shape SingleCellExperiment SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector yaml zlibbioc

Cancer Testis explorer

Julie Devis, Laurent Gatto, Axelle Loriot

Rendered fromCTexploreR.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-10-19
Started: 2023-02-24

Help page	Topics
Gene expression in CCLE Tumors	CCLE_expression
Check spelling of entered variables	check_names
Gene correlations in CCLE cancer cell lines	CT_correlated_genes
CT genes description table	CT_genes
Gene expression in cells treated or not by a demethylating agent	DAC_induction
Gene expression in normal tissues (GTEx)	GTEX_expression
Gene expression in different human cell types	HPA_cell_type_expression
Expression values (TPM) of genes in normal tissues with or without multimapping	normal_tissue_expression_multimapping
Promoter methylation of Cancer-Testis genes in normal tissues	normal_tissues_mean_methylation
Methylation of CpGs located in Cancer-Testis promoters in normal tissues	normal_tissues_methylation
Prepare methylation and expression data of a gene in TCGA tumors	prepare_TCGA_methylation_expression
Determine font size	set_fontsize
Subset databases	subset_database
Gene expression in TCGA tumors	TCGA_expression
Methylation-Expression correlation of Cancer-Testis genes in TCGA samples	TCGA_methylation_expression_correlation
Gene expression in testis cells	testis_expression

Package: CTexploreR 1.1.0

CTexploreR: Explores Cancer Testis Genes

Cancer Testis explorer

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