NEWS

---

coMET 1.29.2 (2022-10-26)

• Remove dependancy colortools
• Add functions to replace the package colortools

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

• -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