CHANGES IN VERSION 2.29.1
-------------------------

* Removing support to legacy archive since it will be shutdown by GDC soon.
* When saving files we will not include folders prefix  legacy/harmonized anymore

CHANGES IN VERSION 2.21.1
-------------------------

* Function GDCPrepare for TARGET-ALL-P3 fixed
* Function getMC3MAF fixed

CHANGES IN VERSION 2.14.0
-------------------------

* Code was rewritten to support projects other than TCGA/TARGET projects
* Add support to STAR counts RNA-Seq
* Add workshops for ATAC-Seq, ELMER, TCGAbiolinks to main vignette
* Function getMC3MAF added to download open MAF file from https://gdc.cancer.gov/about-data/publications/mc3-2017

CHANGES IN VERSION 2.11.2
-------------------------
* Add GISTIC2 case to GDC prepare and manuals

CHANGES IN VERSION 2.7.13
-------------------------
* Adding new function: PanCancerAtlas_subtypes
* Updating DNA methylation probe information function
* Start to update vignette
* FPPE information is being added in GDCprepare
* Minor issue fixes

CHANGES IN VERSION 2.5.0
-------------------------

* Changing chunks.per.download to files.per.chunk

CHANGES IN VERSION 2.2.0
-------------------------

NEW FEATURES
* Add GISTIC2 information and Mutation information in the summarizedExperiment while preparing GDC data

SIGNIFICANT USER-LEVEL CHANGES
* Speed up GDCquery

TCGAbiolinks 2.0
---------------------------------------------------------------
* GDC functions added (GDCquery, GDCdownload, GDCprepare,
GDCquery_Maf, GDCprepare_clinic)
* Removed TCGAquery_investigate, TCGAprofile_plot

TCGAbiolinks 1.3.6
---------------------------------------------------------------
* Starting to move the code to GDC data portal

TCGAbiolinks 1.1.26
---------------------------------------------------------------
* Bug fix: TCGAprepare for  IlluminaHiSeq_miRNASeq platform was
not considering all file types

TCGAbiolinks 1.1.26
---------------------------------------------------------------
* Bug fix: TCGAprepare for  IlluminaHiSeq_miRNASeq platform was
not considering all file types

TCGAbiolinks 1.1.25
---------------------------------------------------------------
* Bug fix: TCGAquery_maf had a bug if only one table was found.
TCGAbiolinks 1.1.24
---------------------------------------------------------------
* Bug fix: types argument for Genome_Wide_SNP_6 was not working.

TCGAbiolinks 1.1.23
---------------------------------------------------------------
* 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 1.1.22
---------------------------------------------------------------
* Bug fix: when  checking the data integrity, manifest was being read
with argument header = T,but it should be false.


TCGAbiolinks 1.1.21
---------------------------------------------------------------
* Improvement: TCGADownload checks for data integrity.

TCGAbiolinks 1.1.20
---------------------------------------------------------------
* Bug fix: TCGAanalyze_Preprocessing subseting was incorrect in case there
were outliers.

TCGAbiolinks 1.1.19
---------------------------------------------------------------
* Bug fix: preparing the data for "IlluminaGA_DNASeq" platform and
TCGAquery_maf had a problem for some files.

TCGAbiolinks 1.1.18
---------------------------------------------------------------
* Update lgg and gbm subtype information. Source: http://dx.doi.org/10.1016/j.cell.2015.12.028

TCGAbiolinks 1.1.17
---------------------------------------------------------------
* Adding batch information to the package. batch.info object is available for user
and TCGAprepare adds automtically info for the summarizedExperiment object
* TCGAvisualize_starburst new parameter: circle, to draw or not the circles in the plot
* Database update

TCGAbiolinks 1.1.16
---------------------------------------------------------------
* Bug fix: subsetByOverlaps was removed from SummarizedExperiment package
TCGAbiolinks should not import it
* Small fixes in documentation
* TCGAanalyze_DMR is now saving the results in a cvs file


TCGAbiolinks 1.1.15
---------------------------------------------------------------
* ggplot2 updat broke the package. Some small fixes were made, but
the function TCGAvisualize_profilePlot is not working as sjPlot is not updated yet.
* small fixes in documentation

TCGAbiolinks 1.1.14
---------------------------------------------------------------
* Change in TCGAvisualize_Heatmap: coloring the columns by patient might give
wrong results if patient has more than one sample in the hetamap.
To solve that we added the possibility to use the sample columns and we added a warning
if there is more than one sample for the patients and a patient column is being used.

TCGAbiolinks 1.1.11 - 1.1.13
---------------------------------------------------------------
* Update in the citation

TCGAbiolinks 1.1.10
----------------------------------------------------------------
* TCGAPrepare: bug fix for bt.exon_quantification files from IlluminaHiSeq_RNASeqV2 platform
* Database update

  TCGAbiolinks 1.1.8
----------------------------------------------------------------
* TCGAvisualize_Heatmap Now it is using Heatmap plus package and is calculating z-cores
* TCGAvisualize_profilePlot  Visualize the distribution of subgroups in the groups distributions
* Database update
* From version 1.0: small bugs corrections in some plots and TCGAprepare_elmer, documentation improvement.

  TCGAbiolinks 0.99.2
----------------------------------------------------------------
  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)
