TCGAbiolinks 1.0.9
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* Bug fix: logFC result from TCGAanalyze_DEA for method "glmLRT" was
considerent the alphabetical order of groups, which migth induce the user to error

TCGAbiolinks 1.0.8
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*  Improvement: TCGADownload checks for data integrity.

  TCGAbiolinks 1.0.7
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* Bugfix in TCGAanalyze_Preprocessing: if there were outliers it was subseeting wrongly.

  TCGAbiolinks 1.0.6
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* Bug fix: preparing the data for "IlluminaGA_DNASeq" platform and
TCGAquery_maf had a problem for some files.
* Added batch information to summarizedExperiment object
* Update lgg and gbm subtype information. Source: http://dx.doi.org/10.1016/j.cell.2015.12.028

  TCGAbiolinks 1.0.5
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* Bugfix: updated ggplot2 code to work with version 2.0

  TCGAbiolinks 1.0.4
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* Improving TCGAquery_clinical to use barcodes.
* Bug fix in TCGAquery_MatchedCoupledSampleTypes
* Bug fix in TCGAPrepare: bt.exon_quantification files from IlluminaHiseq_RNASeqV2 platform was not ok.

  TCGAbiolinks 1.0.2-1.0.3
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* Updating Database
* Updating citation

  TCGAbiolinks 0.99.2
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  FIRST VERSION - FEATURES

* TCGAanalyze_DEA	Differentially expression analysis (DEA) using edgeR 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
* TCGAintegrate	Filtering common samples among platforms from * TCGAquery for the same tumor
* TCGAinvestigate	Find most studied TF in pubmed related to a specific cancer, disease, or tissue
* TCGAprepare	Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object.
* 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_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_Version	Shows a summary (version, date, number of samples, size of the data) of all versions of data for a given tumor and platform.
* TCGAsocial	Finds the number of downloads of a package on CRAN or BIOC and find questions in website ("bioconductor.org", "biostars.org", "stackoverflow).
* TCGAvisualize_EAbarplot	barPlot for a complete Enrichment Analysis
* 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)