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