CHANGES in VERSION 2.1.9 - add `getKEGGGenome()` ------------------------------------------ CHANGES in VERSION 2.1.8 - add `getGenomeDateFromNCBI()` ------------------------------------------- CHANGES in VERSION 2.1.4 * online great: the names of input regions are kept. * region coordinates (1-based or zero-based) are adjusted in `getRegionGeneAssociations()`. ------------------------------------------- CHANGES in VERSION 1.99.7 * Calculation has been speeded up. -------------------------------------------- CHANGES in VERSION 1.99.6 * set `getGeneSetsFromBioMart()` public --------------------------------------------- CHANGES in VERSION 1.99.2 * by default exclude gap regions * chr prefix in `gr` is removed when `biomart_dataset` is set. ----------------------------------------------- CHANGES in VERSION 1.99.0 * add `great()` and related functions to support local GREAT. * add `shinyReport()` to export results into a shiny application. ----------------------------------------------- CHANGES in VERSION 1.21.1 * parseRegionGeneAssociationFile(): parsing also considers positions with no sign. ----------------------------------------------- CHANGES in VERSION 1.19.1 * add 'tsv' option in `getEnrichmentTables()` ------------------------------------------------ CHANGES in VERSION 1.17.1 * assign to foreName and backName when querying GREAT * use rmarkdown for vignette * support GREAT version 4.0.4 * add startup messages ------------------------------------------------ CHANGES in VERSION 1.15.1 * `plotRegionGeneAssociationGraphs()`: fixe a bug of wrong value of `par(mfrow)`. * fixed warnings of Rd files. ------------------------------------------------- CHANGES in VERSION 1.13.3 * parse error message from GREAT --------------------------------------------------- CHANGES in VERSION 1.13.1 * `plotRegionGeneAssociationGraphs()`: `par(mfrow)` is automatically set according to the length of `type`. ---------------------------------------------------- CHANGES in VERSION 1.11.1 * save regions in gzip file then submit to GREAT * will not change the content of the input regions ---------------------------------------------------- CHANGES in VERSION 1.9.1 * change url according to changes on GREAT website ----------------------------------------------------- CHANGES in VERSION 1.7.1 * submitGreatJob(): remove additional column by pintersect() ----------------------------------------------------- CHANGES in VERSION 1.5.3 * if background is provided, input regions are automaticially adjusted to make sure all input regions are subset of backgrounds. ------------------------------------------------------ CHANGES in VERSION 1.3.3 * documentations were improved. * test files are moved to tests/testthat -------------------------------------------------------- CHANGES in VERSION 1.3.2 * bug fixed when background is self-provided. -------------------------------------------------------- CHANGES in VERSION 1.3.1 * fixed a bug when gene symbol annotated by GREAT is '' * print warnings when GREAT gives warnings -------------------------------------------------------- CHANGES in VERSION 1.1.6 * versions of GREAT can be selected -------------------------------------------------------- CHANGES in VERSION 1.1.5 * minor changes in documentations --------------------------------------------------------- CHANGES in VERSION 1.1.4 * minor changes to adjust to github mirror ---------------------------------------------------------- CHANGES in VERSION 1.1.3 * error message is extract from GREAT now. * default value of `bgChoice` depeneds on `gr` ----------------------------------------------------------- CHANGES in VERSION 1.1.2 * add dependency to base packages ----------------------------------------------------------- CHANGES in VERSION 1.1.1 * enrivonment for the slots in `GreatJob` object are initialized inside `submitGreatJob` ----------------------------------------------------------- CHANGES IN VERSION 0.99.5 * because analysis depends on internet connection, jump to next version to enforce rebuilding of the vignette on bioconductor. ------------------------------------------------------------ CHANGES IN VERSION 0.99.4 * retrieve categories and corresponding ontologies from GREAT ------------------------------------------------------------