Package: TCGAbiolinks 2.35.0

Tiago Chedraoui Silva

TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides 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 easily develop complete analysis pipelines.

Authors:Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot, Tathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr

TCGAbiolinks_2.35.0.tar.gz
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TCGAbiolinks.pdf |TCGAbiolinks.html✨
TCGAbiolinks/json (API)
NEWS

# Install 'TCGAbiolinks' in R:

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

Bug tracker:https://github.com/bioinformaticsfmrp/tcgabiolinks/issues

Datasets:

TabSubtypesCol_merged - TCGA samples with their Pam50 subtypes
Tumor.purity - TCGA samples with their Tumor Purity measures

On BioConductor:TCGAbiolinks-2.35.0(bioc 3.21)TCGAbiolinks-2.34.0(bioc 3.20)

dnamethylation differentialmethylation generegulation geneexpression methylationarray differentialexpression pathways network sequencing survival software bioc bioconductor gdc integrative-analysis tcga tcga-data tcgabiolinks

14.58 score 298 stars 6 packages 1.6k scripts 6.5k downloads 276 mentions 57 exports 105 dependencies

Last updated 21 days agofrom:cd39121b7f. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	WARNING	Nov 19 2024
R-4.5-linux	WARNING	Nov 19 2024
R-4.4-win	WARNING	Nov 19 2024
R-4.4-mac	ERROR	Nov 19 2024
R-4.3-win	WARNING	Nov 19 2024
R-4.3-mac	ERROR	Nov 19 2024

Exports:colDataPrepare gaiaCNVplot GDCdownload GDCprepare GDCprepare_clinic GDCquery GDCquery_ATAC_seq GDCquery_clinic get_IDs get.GRCh.bioMart getAdjacencyBiogrid getDataCategorySummary getGDCInfo getGDCprojects getGistic getLinkedOmicsData getManifest getMC3MAF getProjectSummary getResults getSampleFilesSummary gliomaClassifier isServeOK matchedMetExp PanCancerAtlas_subtypes TCGA_MolecularSubtype TCGAanalyze_analyseGRN TCGAanalyze_Clustering TCGAanalyze_DEA TCGAanalyze_DEA_Affy TCGAanalyze_DMC TCGAanalyze_EAcomplete TCGAanalyze_Filtering TCGAanalyze_LevelTab TCGAanalyze_networkInference TCGAanalyze_Normalization TCGAanalyze_Pathview TCGAanalyze_Preprocessing TCGAanalyze_Stemness TCGAanalyze_survival TCGAanalyze_SurvivalKM TCGAbatch_Correction TCGAprepare_Affy TCGAquery_MatchedCoupledSampleTypes TCGAquery_recount2 TCGAquery_SampleTypes TCGAquery_subtype TCGAtumor_purity TCGAvisualize_BarPlot TCGAvisualize_EAbarplot TCGAvisualize_Heatmap TCGAvisualize_meanMethylation TCGAvisualize_oncoprint TCGAvisualize_PCA TCGAvisualize_starburst TCGAVisualize_volcano UseRaw_afterFilter

Dependencies:abind AnnotationDbi askpass Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob cachem cli clipr colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray digest downloader dplyr evaluate fansi farver fastmap filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable highr hms httr httr2 IRanges isoband jsonlite KEGGREST knitr labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png prettyunits progress purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp readr rlang RSQLite rvest S4Arrays S4Vectors scales selectr SparseArray stringi stringr SummarizedExperiment sys TCGAbiolinksGUI.data tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

Introduction

Rendered fromindex.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-04-01
Started: 2017-02-06

TCGAbiolinks version bump with new functions

Mohamed Mounir

Rendered fromextension.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2019-03-18
Started: 2018-01-04

TCGAbiolinks: Searching GDC database

Rendered fromquery.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-05-18
Started: 2017-02-06

TCGAbiolinks: Downloading and preparing files for analysis

Rendered fromdownload_prepare.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-05-06
Started: 2017-02-06

TCGAbiolinks: Clinical data

Rendered fromclinical.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-05-18
Started: 2017-02-06

TCGAbiolinks: Searching, downloading and visualizing mutation files

Rendered frommutation.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-05-08
Started: 2017-02-06

Classifiers methods

Rendered fromclassifiers.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-10-05
Started: 2019-11-27

Stemness score

Rendered fromstemness_score.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-05-13
Started: 2022-04-18

Compilation of TCGA molecular subtypes

Rendered fromsubtypes.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-05-05
Started: 2018-01-05

Analyzing and visualizing TCGA data

Rendered fromanalysis.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2023-05-08
Started: 2018-01-05

Case Studies

Rendered fromcasestudy.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-08-12
Started: 2018-01-05

Help page	Topics
Create samples information matrix for GDC samples	colDataPrepare
Perform non-parametrix wilcoxon test	dmc.non.parametric
Creates a plot for GAIA output (all significant aberrant regions.)	gaiaCNVplot
Download GDC data	GDCdownload
Prepare GDC data	GDCprepare
Parsing clinical xml files	GDCprepare_clinic
Query GDC data	GDCquery
Retrieve open access ATAC-seq files from GDC server	GDCquery_ATAC_seq
Get GDC clinical data	GDCquery_clinic
Extract information from TCGA barcodes.	get_IDs
Get hg19 gene annotation or hg38 (gencode v36)	get.GRCh.bioMart
Get a matrix of interactions of genes from biogrid	getAdjacencyBiogrid
Create a Summary table for each sample in a project saying if it contains or not files for a certain data category	getDataCategorySummary
Check GDC server status	getGDCInfo
Retrieve all GDC projects	getGDCprojects
Download GISTIC data from firehose	getGistic
Retrieve linkedOmics data	getLinkedOmicsData
Get a Manifest from GDCquery output that can be used with GDC-client	getManifest
Retrieve open access mc3 MAF file from GDC server	getMC3MAF
Get Number of cases in GDC for a project	getNbCases
Get Number of files in GDC for a project	getNbFiles
Get Project Summary from GDC	getProjectSummary
Get the results table from query	getResults
Retrieve summary of files per sample in a project	getSampleFilesSummary
getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.	getTSS
Gliomar classifier	gliomaClassifier
Check GDC server status is OK	isServeOK
Get GDC primary tumors samples with both DNA methylation (HM450K) and Gene expression data	matchedMetExp
Retrieve table with TCGA molecular subtypes	PanCancerAtlas_subtypes
internal function to break a huge API call into smaller ones so it repects the max character limit of a string	splitAPICall
TCGA samples with their Pam50 subtypes	TabSubtypesCol_merged
Retrieve molecular subtypes for given TCGA barcodes	TCGA_MolecularSubtype
Generate network	TCGAanalyze_analyseGRN
Hierarchical cluster analysis	TCGAanalyze_Clustering
Differential expression analysis (DEA) using edgeR or limma package.	TCGAanalyze_DEA
Differentially expression analysis (DEA) using limma package.	TCGAanalyze_DEA_Affy
Differentially methylated regions Analysis	TCGAanalyze_DMC
Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways.	TCGAanalyze_EA
Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways	TCGAanalyze_EAcomplete
Filtering mRNA transcripts and miRNA selecting a threshold.	TCGAanalyze_Filtering
Adding information related to DEGs genes from DEA as mean values in two conditions.	TCGAanalyze_LevelTab
infer gene regulatory networks	TCGAanalyze_networkInference
normalization mRNA transcripts and miRNA using EDASeq package.	TCGAanalyze_Normalization
Generate pathview graph	TCGAanalyze_Pathview
Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier	TCGAanalyze_Preprocessing
Generate Stemness Score based on RNASeq (mRNAsi stemness index) Malta et al., Cell, 2018	TCGAanalyze_Stemness
Creates survival analysis	TCGAanalyze_survival
survival analysis (SA) univariate with Kaplan-Meier (KM) method.	TCGAanalyze_SurvivalKM
Batch correction using ComBat and Voom transformation using limma package.	TCGAbatch_Correction
Prepare CEL files into an AffyBatch.	TCGAprepare_Affy
Retrieve multiple tissue types from the same patients.	TCGAquery_MatchedCoupledSampleTypes
Query gene counts of TCGA and GTEx data from the Recount2 project	TCGAquery_recount2
Retrieve multiple tissue types not from the same patients.	TCGAquery_SampleTypes
Retrieve molecular subtypes for a given tumor	TCGAquery_subtype
Filters TCGA barcodes according to purity parameters	TCGAtumor_purity
Barplot of subtypes and clinical info in groups of gene expression clustered.	TCGAvisualize_BarPlot
barPlot for a complete Enrichment Analysis	TCGAvisualize_EAbarplot
Heatmap with more sensible behavior using heatmap.plus	TCGAvisualize_Heatmap
Mean methylation boxplot	TCGAvisualize_meanMethylation
Creating a oncoprint	TCGAvisualize_oncoprint
Principal components analysis (PCA) plot	TCGAvisualize_PCA
Create starburst plot	TCGAvisualize_starburst
Survival analysis with univariate Cox regression package (dnet)	TCGAvisualize_SurvivalCoxNET
Creates a volcano plot for DNA methylation or gene expression	TCGAVisualize_volcano
TCGA samples with their Tumor Purity measures	Tumor.purity
Use raw count from the DataPrep object which genes are removed by normalization and filtering steps.	UseRaw_afterFilter