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
o Add GISTIC2 information and Mutation information in the summarizedExperiment while preparing GDC data
SIGNIFICANT USER-LEVEL CHANGES
o 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)