COMET 1.27.2 - 2022-04-18
------------------------
- Update ENSEMBL functions for https
- Remove DNase_UCSC functions
- Add information about font.family for plotTrack and other Gviz functions
- Add showtext library in coMET.Rnw vignette

COMET 1.23.1 - 2021-05-16
-------------------------
- Update datasets with Biomart
For example:
data(allIG)
allIG@biomart@httr_config <- list()
save(allIG,file="XXXX")

COMET 1.15.2 - 2018-12-24
-------------------------
- Update vignette (add warning=False)

COMET 1.15.1 - 2018-12-24
-------------------------
- Update script to snp_ensembL

COMET 1.11.5 - 2018-04-11
-------------------------
- Update vignettes

COMET 1.11.4 - 2018-03-28
-------------------------
- Update examples in manual because change of functions
- Put some functions obselete because change of database (such as COSMIC, regulatory segment ENSEMBL, ISCA)
- remove R package, ggplot2, ggbio and trackviewer

COMET 1.11.3 - 2018-02-25
-------------------------
- Update vignette because of the update of BiocStyle
- Update two data (chipTFtrack.rda and genesGencodetrack.rda) because error formating

COMET 1.11.1 - 2017-07-27
-------------------------
- Update vignette because of the update of BiocStyle
- Add examples data that was not uploaded correctly the first time

COMET 1.5.5 - 2016-06-12
-------------------------
- Update the script for coMET website
- remove big files
- Add examples data that was not uploaded correctly the first time

COMET 1.5.3 - 2016-06-8
-------------------------
-Change the name of functions:
  xenorefGenesUCSC into xenorefGenes_UCSC
  transcriptENSEMBL into transcript_ENSEMBL
  structureBiomart into structureBiomart_ENSEMBL
  snpLocationsUCSC into snpLocations_UCSC
  snpBiomart into snpBiomart_ENSEMBL
  RepeatMaskerTrack into repeatMasker_UCSC
  regulationBiomart into regulationBiomart_ENSEMBL
  knownGenesUCSC into knownGenes_UCSC
  ISCATrack into ISCA_UCSC
  HistoneOne into HistoneOne_UCSC
  HistoneAll to HistoneAll_UCSC
  GWASTrack to GWAScatalog_UCSC
  genesNameENSEMBL to genesName_ENSEMBL
  genesENSEMBL to genes_ENSEMBL
  GeneReviewsTrack to GeneReviews_UCSC
  gcContent to gcContent_UCSC
  GADTrack to GAD_UCSC
  DNAseUCSC to DNAse_UCSC
  COSMICTrack to COSMIC_UCSC
  cpgIslandsUCSC to cpgIslands_UCSC
  CoreillCNVTrack to CoreillCNV_UCSC
  chromatinHMMAll to chromatinHMMAll_UCSC
  chromatinHMMOne to chromatinHMMOne_UCSC
  ClinVarCnvTrack to ClinVarCnv_UCSC
  ClinVarMainTrack to ClinVarMain_UCSC

COMET 1.4.3 - 2016-04-29
-------------------------
- Update the management of multiple secondary info data
- Add the update done in the devel version that was not updated in the new release for x reasons

COMET 1.3.1 - 2016-04-06
-------------------------
- update for new version of Bioconductor

COMET 1.0.3 - 2015-12-06
-------------------------
- Add functions to visualise data from FANTOM, GeTEX and Hi-C data
- Update the vignette related to these new functions

COMET 1.0.2 - 2015-08-10
-------------------------
- Add the option to visualise beta values in changing the size of symbole relative to the absolue value of beta valuein the top of plot
- Visualisation of RoadMap data for chrommHMM for specific tissues
- Visualisation of metQTL data and of eQTL data

COMET 1.0.1 - 2015-07-10
-------------------------
- Update the vignette (need to install the package psych, command line to check the new package before upload on bioconductor)
- New functions for annotation tracks (4 functions related to Regulation ENSEMBL biomart, 1 related to UCSC [segmental duplications])
- New functions for change colors in genesENSEMBL and transciptENSEMBL called interestGenesENSEMBL and interestTranscriptENSEMBL
- Correction for uppercase to lowcase for the word "ASSO" related to the option disp.association
- New dataset related to new functions

COMET 1.0.0 - 2015-04-15
-------------------------
- Enter in the stable release of Bioconductor

COMET 0.99.10 - 2015-04-10
-------------------------
- Update regulationBiomart function and the pre-computed data associated because ENSEMBL has recently updated their schema in Biomart for these data.
- Update the documentations (man and vignette)

COMET 0.99.9 - 2015-03-10
-------------------------
- Update snpBiomart and structureBiomart functions and the pre-computed data associated because ENSEMBL has recently updated their schema in Biomart for these data.
- Update the documentations (man and vignette)
- Add the function compute.pvalue.cormatrix and allow the visualisation of only correlation under a significant level. (use the library psych)
- Add the function comet.list to list the correlations between omic features
- Replace capital letter by low letter
- Update Shiny-based web application according to new functions

COMET 0.99.8 - 2015-02-15
-----------------------------
- Correction genesNameENSEMBL in order not to run if no ENSEMBL gene in the region of interest
- Correction the error related to the loading of correlation matrice
- Update the visualisation of Chromosome with the name of band (related to an update of Gviz)
- Remove the visualisation of border for genes and transcripts to help the visualisation of different exons
- Update the vignette about comet's Shiny website and colors of tracks
- Update the annotation tracks as Gviz was updated and now coMET can work on Gviz (version 1.10.9, current version)

COMET 0.99.7 - 2014-12-19
-----------------------------
- Update the function "genesENSEMBL", "genesNameENSEMBL", "transcriptENSEMBL", and "regulationBiomart" because ENSEMBL mart changed the names of field in GChr37


COMET 0.99.6 - 2014-11-25
-----------------------------
- add in "import IRanges and S4Vectors" in NAMESPACE
- Fix mistakes in the vignette


COMET 0.99.5 - 2014-11-06
-----------------------------
- Update the annotation tracks using Gviz because of the update of Gviz (version 1.11.2, development version)

COMET 0.99.4 - 2014-11-05
-----------------------------
- Update the manual and the vignette
- Fix little bugs
- Update the annotation tracks using BiomartGeneRegionTrack of Gviz


COMET 0.99.3 - 2014-10-25
-----------------------------
- Update the manuel and the vignette
- Update the function to create annotation tracks connecting to ENSEMBL mart (change of schema)
- Fix little bug
- Add the function to define the reference genome (cf the change of schema of ENSEMBL mart)


COMET 0.99.2 - 2014-10-16
-----------------------------

- Update the manual comet.web file

COMET 0.99.1 - 2014-10-16
-----------------------------

- Add the package "BiocStyle" in Suggests of DESCRIPTION file
- Change the absolute path to relative path of files (info file, expression file, and correlation file) in vignette and manual


COMET 0.99.0 - 2014-09-24
-----------------------------

- Version draft of this script
