NEWS

---

rGREAT 2.5.2

• add 'getGeneSetsFromOrgDb()'

rGREAT 2.5.1

• support extending from the whole genes

rGREAT 2.1.9

• add 'getKEGGGenome()'

rGREAT 2.1.8

• add 'getGenomeDateFromNCBI()'

rGREAT 2.1.4

• online great: the names of input regions are kept.
• region coordinates (1-based or zero-based) are adjusted in 'getRegionGeneAssociations()'.

rGREAT 1.99.7

• Calculation has been speeded up.

rGREAT 1.99.6

• set 'getGeneSetsFromBioMart()' public

rGREAT 1.99.2

• by default exclude gap regions
• chr prefix in 'gr' is removed when 'biomart_dataset' is set.

rGREAT 1.99.0

• add 'great()' and related functions to support local GREAT.
• add 'shinyReport()' to export results into a shiny application.

rGREAT 1.21.1

• parseRegionGeneAssociationFile(): parsing also considers positions with no sign.

rGREAT 1.19.1

• add 'tsv' option in 'getEnrichmentTables()'

rGREAT 1.17.1

• assign to foreName and backName when querying GREAT
• use rmarkdown for vignette
• support GREAT version 4.0.4
• add startup messages

rGREAT 1.15.1

• 'plotRegionGeneAssociationGraphs()': fixe a bug of wrong value of 'par(mfrow)'.
• fixed warnings of Rd files.

rGREAT 1.13.3

• parse error message from GREAT

rGREAT 1.13.1

• 'plotRegionGeneAssociationGraphs()': 'par(mfrow)' is automatically set according to the length of 'type'.

rGREAT 1.11.1

• save regions in gzip file then submit to GREAT
• will not change the content of the input regions

rGREAT 1.9.1

• change url according to changes on GREAT website

rGREAT 1.7.1

• submitGreatJob(): remove additional column by pintersect()

rGREAT 1.5.3

• if background is provided, input regions are automaticially adjusted to make sure all input regions are subset of backgrounds.

rGREAT 1.3.3

• documentations were improved.
• test files are moved to tests/testthat

rGREAT 1.3.2

• bug fixed when background is self-provided.

rGREAT 1.3.1

• fixed a bug when gene symbol annotated by GREAT is ”
• print warnings when GREAT gives warnings

rGREAT 1.1.6

• versions of GREAT can be selected

rGREAT 1.1.5

• minor changes in documentations

rGREAT 1.1.4

• minor changes to adjust to github mirror

rGREAT 1.1.3

• error message is extract from GREAT now.
• default value of 'bgChoice' depeneds on 'gr'

rGREAT 1.1.2

• add dependency to base packages

rGREAT 1.1.1

• enrivonment for the slots in 'GreatJob' object are initialized inside 'submitGreatJob'

rGREAT 0.99.5

• because analysis depends on internet connection, jump to next version to enforce rebuilding of the vignette on bioconductor.

rGREAT 0.99.4

• retrieve categories and corresponding ontologies from GREAT