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TCGAbiolinks: An R/Bioconductor package for integrative analysis withTCGA data

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Yes, there is a problem with the package versions you are using. When you post a question here it is normally expected that you will be using the current release of Bioconductor. Your packages are two Bioconductor releases out of date. You are using Bioconductor 3.10 instead of Bioconductor 3.12. And the sessionInfoare as followings: sessionInfo R version 3.5.2 (2018-12-20) Platform: x8664-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.1. Bioconductor Resources. An Introduction to R and Bioconductor. Includes information about installation and getting help. Basic Introduction to R and Bioconductor; Bioconductor Courses; An excellent starter to Affymetrix data analysis Jean Wu’s excellent lab on Affymetrix data analysis; Guide to importing GEO soft data files into bioconductor.

The aim of TCGAbiolinks is : i) facilitate the TCGA open-accessdata retrieval, ii) prepare the data using the appropriate pre-processingstrategies, iii) provide the means to carry out different standard analysesand iv) allow the user to download a specific version of the data and thusto easily reproduce earlier research results. In more detail, the packageprovides multiple methods for analysis (e.g., differential expression analysis,identifying differentially methylated regions) and methods for visualization(e.g., survival plots, volcano plots, starburst plots) in order to easilydevelop complete analysis pipelines.

Set some options and make sure the packages edgeR, gplots, RColorBrewer, topGO, KEGGREST, Rgraphviz and org.Hs.eg.db are installed (if not install it), and then load. In the R console run the following commands. Heatplot calls heatmap.2 in the R package gplots. NOTE: We have changed heatplot scaling in made4 (v 1.19.1) in Bioconductor v2.5. Heatplot by default dual scales the data to limits of -3,3. To reproduce older version of heatplot, use the parameters dualScale=FALSE, scale='row'.

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Functions in TCGAbiolinks

Name Description
PR_status_BRCAPR_status_BRCA
TCGAvisualize_meanMethylationMean methylation boxplot
TCGAanalyze_DEA_AffyDifferentially expression analysis (DEA) using limma package.
TCGAvisualize_oncoprintCreating a oncoprint
TCGAquery_clinicGet the clinical information
TCGAprepare_AffyPrepare CEL files into an AffyBatch.
tabPackage2tabPackage2
TCGAquery_subtypeRetrieve molecular subtypes for a given tumor
TCGAquery_MatchedCoupledSampleTypesRetrieve multiple tissue types from the same patients.
TCGAprepare_elmerPrepare the data for ELEMR package
BRCA_rnaseqv2BRCA_rnaseqv2
TCGAanalyze_SurvivalKMsurvival analysis (SA) univariate with Kaplan-Meier (KM) method.
TCGAvisualize_SurvivalCoxNETSurvival analysis with univariate Cox regression package (dnet)
TCGAanalyze_EAcompleteEnrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways
dataREAD_dfTCGA data matrix READ
tabSurvKMcompleteDEGstabSurvKMcompleteDEGs
TCGAanalyze_ClusteringHierarchical cluster analysis
ER_status_BRCAER_status_BRCA
HER_status_BRCAHER_status_BRCA
TCGAdownloadDownload the data from TCGA using as reference the output from TCGAquery
TCGAanalyze_PreprocessingArray Array Intensity correlation (AAIC) and correlation boxplot to define outlier
TCGAanalyze_DMRDifferentially methylated regions Analysis
TCGAvisualize_BarPlotBarplot of subtypes and clinical info in groups of gene expression clustered.
ggbiplotBiplot for Principal Components using ggplot2
geneInfogeneInfo for normalization
TCGAUpdateTCGAUpdate
TCGAvisualize_profilePlotProfile plot
TCGAbiolinksDownload data of samples from TCGA
TCGAanalyze_EAEnrichment analysis of a gene-set with GO [BP,MF,CC] and pathways.
diffmeanCalculate diffmean methylation between two groups
TCGAanalyze_FilteringFiltering mRNA transcripts and miRNA selecting a threshold.
tabPackageKeytabPackageKey
TCGAquery_clinicFiltFilter samples using clinical data
TCGAquery_SampleTypesRetrieve multiple tissue types not from the same patients.
clinBRCAClinical data TCGA BRCA
TCGAvisualize_HeatmapHeatmap with more sensible behavior using heatmap.plus
TCGAprepareRead the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.
dataBRCATCGA data matrix BRCA
TCGAquery_mafGet last maf file for the tumor
gender_BRCAgender_BRCA
stage_BRCAstage_BRCA
TCGAvisualize_TablesVisaulize results in format of latex tables.
TCGAanalyze_DEADifferentially expression analysis (DEA) using edgeR package.
batch.infoTCGA batch information from Biospecimen Metadata Browser
TCGAquery_SocialFinds the number of downloads of a package on CRAN or BIOC andfind questions in website ('bioconductor.org', 'biostars.org', 'stackoverflow).
TCGAvisualize_EAbarplotbarPlot for a complete Enrichment Analysis
TCGAvisualize_starburstCreate starburst plot
TCGAvisualize_PCAPrincipal components analysis (PCA) plot
tabDEGsTFPubmedTCGA data matrix BRCA DEGs Pubmed
BRCA_RNASeqV2_versionTCGA Table with version, number of samples and size (Mbyte) ofBRCA IlluminaHiSeq_RNASeqV2 Level 3
GeneSplitRegulonGeneSplitRegulon
TCGAVisualize_volcanoCreates a volcano plot for DNA methylation or expression
TCGAanalyze_survivalCreates survival analysis
TCGAquery_VersionShows a summary (version, date, number of samples, size of the data) ofall versions of data for a given tumor and platform.
TCGAquery_samplesfilterFiltering sample output from TCGAquery
TCGAquery_integrateFiltering common samples among platforms from TCGAquery for the same tumor
TCGAvisualize_mutationVisualize mutation
dataDEGsFiltLevelTCGA data matrix BRCA DEGs
clinical_data_site_cancerclinical_data_site_cancer
calculate.pvaluesCalculate pvalues
dataREADTCGA data SummarizedExperiment READ
GenesCutIDGenesCutID
TCGAanalyze_Normalizationnormalization mRNA transcripts and miRNA using EDASeq package.
TCGAquery_InvestigateFind most studied TF in pubmed related to a specific cancer, disease, or tissue
TCGAquerySearches TCGA open-access data providing also latest version of the files.
TCGAanalyze_LevelTabAdding information related to DEGs genes from DEA as mean values in two conditions.
tabPackage1tabPackage1
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Details

TypePackage
Date2015-12-13
LicenseGPL (>= 3)
biocViewsDNAMethylation,DifferentialMethylation,GeneRegulation,GeneExpression,MethylationArray,DifferentialExpression,Pathways,Network,Survival
VignetteBuilderknitr
LazyDatatrue
URLhttps://github.com/BioinformaticsFMRP/TCGAbiolinks
BugReportshttps://github.com/BioinformaticsFMRP/TCGAbiolinks/issues
RoxygenNote5.0.1
imports affy , Biobase , BiocGenerics , biomaRt , circlize , coin , ComplexHeatmap , ConsensusClusterPlus , cowplot , data , data.table , dnet , doParallel , downloader (>= 0.4) , dplyr , EDASeq (>= 2.0.0) , edgeR (>= 3.0.0) , genefilter , GenomicFeatures , GenomicRanges , GGally , ggplot2 , ggrepel , ggthemes , gplots , graphics , grDevices , gtable , httr , igraph , IRanges , knitr , limma , magrittr , matlab , parallel , plyr , RColorBrewer , RCurl , reshape2 , rjson , rvest (>= 0.3.0) , S4Vectors , scales , sjmisc , sjPlot (>= 2.0) , stats , stringr (>= 1.0.0) , SummarizedExperiment , supraHex , survival , TxDb , TxDb.Hsapiens.UCSC.hg19.knownGene , utils , XML , xml2 , xtable
depends base (>= 3.2) , R (>= 3.2)
suggests BiocStyle , devtools , png , rmarkdown , testthat
ContributorsMichele Ceccarelli, Houtan Noushmehr, Isabella Castiglioni, Davide Garolini, Thais Sabedot, Tathiane Malta, Catharina Olsen, Gianluca Bontempi, Stefano Pagnotta, Luciano Garofano, Antonio Colaprico, Tiago Silva, Claudia Cava

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