TCGAbiolinks-package |
Download data of samples from TCGA |
TCGAanalyze_Clustering |
Hierarchical cluster analysis |
TCGAanalyze_copynumber |
Identifying Segment Gain Or Loss (SGOL) |
TCGAanalyze_DEA |
Differentially expression analysis (DEA) using edgeR package. |
TCGAanalyze_DEA_Affy |
Differentially expression analysis (DEA) using limma package. |
TCGAanalyze_DMR |
Differentially methylated regions Analysis |
TCGAanalyze_EA |
Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways. |
TCGAanalyze_EAcomplete |
Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways |
TCGAanalyze_Filtering |
Filtering mRNA transcripts and miRNA selecting a threshold. |
TCGAanalyze_LevelTab |
Adding information related to DEGs genes from DEA as mean values in two conditions. |
TCGAanalyze_Normalization |
normalization mRNA transcripts and miRNA using EDASeq package. |
TCGAanalyze_Preprocessing |
Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier |
TCGAanalyze_survival |
Creates survival analysis |
TCGAanalyze_SurvivalKM |
survival analysis (SA) univariate with Kaplan-Meier (KM) method. |
TCGAbiolinks |
Download data of samples from TCGA |
TCGAdownload |
Download the data from TCGA using as reference the output from TCGAquery |
TCGAprepare |
Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object. |
TCGAprepare_Affy |
Prepare CEL files into an AffyBatch. |
TCGAprepare_elmer |
Prepare the data for ELEMR package |
TCGAquery |
Searches TCGA open-access data providing also latest version of the files. |
TCGAquery_clinic |
Get the clinical information |
TCGAquery_clinicFilt |
Filter samples using clinical data |
TCGAquery_integrate |
Filtering common samples among platforms from TCGAquery for the same tumor |
TCGAquery_Investigate |
Find most studied TF in pubmed related to a specific cancer, disease, or tissue |
TCGAquery_maf |
Get last maf file for the tumor |
TCGAquery_MatchedCoupledSampleTypes |
Retrieve multiple tissue types from the same patients. |
TCGAquery_samplesfilter |
Filtering sample output from TCGAquery |
TCGAquery_SampleTypes |
Retrieve multiple tissue types not from the same patients. |
TCGAquery_Social |
Finds the number of downloads of a package on CRAN or BIOC and find questions in website ("bioconductor.org", "biostars.org", "stackoverflow). |
TCGAquery_subtype |
Retrieve molecular subtypes for a given tumor |
TCGAquery_Version |
Shows a summary (version, date, number of samples, size of the data) of all versions of data for a given tumor and platform. |
TCGAvisualize_BarPlot |
Barplot of subtypes and clinical info in groups of gene expression clustered. |
TCGAvisualize_EAbarplot |
barPlot for a complete Enrichment Analysis |
TCGAvisualize_Heatmap |
Heatmap with more sensible behavior using heatmap.plus |
TCGAvisualize_meanMethylation |
Mean methylation boxplot |
TCGAvisualize_PCA |
Principal components analysis (PCA) plot |
TCGAvisualize_starburst |
Create starburst plot |
TCGAvisualize_SurvivalCoxNET |
Survival analysis with univariate Cox regression package (dnet) |
TCGAvisualize_Tables |
Visaulize results in format of latex tables. |
TCGAVisualize_volcano |
Creates a volcano plot for DNA methylation or expression |