Package: CTexploreR 1.3.0

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_1.3.0.tar.gz
CTexploreR_1.3.0.zip(r-4.5)CTexploreR_1.3.0.zip(r-4.4)
CTexploreR_1.3.0.tgz(r-4.4-any)
CTexploreR_1.3.0.tar.gz(r-4.5-noble)CTexploreR_1.3.0.tar.gz(r-4.4-noble)
CTexploreR_1.3.0.tgz(r-4.4-emscripten)
CTexploreR.pdf |CTexploreR.html✨
CTexploreR/json (API)
NEWS

# Install 'CTexploreR' in R:
install.packages('CTexploreR', repos = c('https://uclouvain-cbio.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On BioConductor:CTexploreR-1.1.2(bioc 3.21)CTexploreR-1.2.0(bioc 3.20)

transcriptomicsepigeneticsdifferentialexpressiongeneexpressiondnamethylationexperimenthubsoftwaredataimportbioconductor

5.13 score 2 scripts 20 exports 100 dependencies

Last updated 24 days agofrom:b8dffc614f. Checks:OK: 4 WARNING: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winOKNov 05 2024
R-4.5-linuxWARNINGNov 05 2024
R-4.4-winOKNov 05 2024
R-4.4-macOKNov 05 2024

Exports:all_genesCCLE_expressionCT_correlated_genesCT_genesDAC_inductionembryo_expressionembryos_mean_methylationfetal_germcells_expressionfetal_germcells_mean_methylationGTEX_expressionhESC_expressionhESC_mean_methylationHPA_cell_type_expressionnormal_tissue_expression_multimappingnormal_tissues_mean_methylationnormal_tissues_methylationoocytes_expressionTCGA_expressionTCGA_methylation_expression_correlationtestis_expression

Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayonCTdatacurlDBIdbplyrDelayedArraydigestdoParalleldplyrExperimentHubfansifarverfastmapfilelockforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngpurrrR6rappdirsRColorBrewerRcpprjsonrlangRSQLiteS4ArraysS4VectorsscalesshapeSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectoryamlzlibbioc

Cancer Testis explorer

Julie Devis, Laurent Gatto, Axelle Loriot

Rendered fromCTexploreR.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-10-28
Started: 2023-02-24

Readme and manuals

Help Manual

Help pageTopics
All genes description tableall_genes
Gene expression in CCLE TumorsCCLE_expression
Check spelling of entered variablescheck_names
Gene correlations in CCLE cancer cell linesCT_correlated_genes
CT genes description tableCT_genes
Gene expression in cells treated or not by a demethylating agentDAC_induction
Gene expression in human embryosembryo_expression
Promoter methylation of any gene in early embryosembryos_mean_methylation
Gene expression in fetal germ cellsfetal_germcells_expression
Promoter methylation of any gene in fetal germ cellsfetal_germcells_mean_methylation
Gene expression in normal tissues (GTEx)GTEX_expression
Gene expression in human embryonic stem cellshESC_expression
Promoter methylation of any gene in hESChESC_mean_methylation
Gene expression in different human cell typesHPA_cell_type_expression
Expression values (TPM) of genes in normal tissues with or without multimappingnormal_tissue_expression_multimapping
Promoter methylation of any gene in normal tissuesnormal_tissues_mean_methylation
Methylation of CpGs located in promoters in normal tissuesnormal_tissues_methylation
Gene expression in oocytesoocytes_expression
Prepare methylation and expression data of a gene in TCGA tumorsprepare_TCGA_methylation_expression
Determine font sizeset_fontsize
Subset databasessubset_database
Gene expression in TCGA tumorsTCGA_expression
Methylation-Expression correlation of any genes in TCGA samplesTCGA_methylation_expression_correlation
Gene expression in testis cellstestis_expression