Version 0.99.0

Initial package submitted.

Version 0.99.2

Codes:

Added calls to match.args() for partial matching.
Added calls to isTRUE() for checking logical inputs.
Replaces cat() with message().

Vignette:

Tabs are replaced by spaces.
Added some math notations.

R Dependency:

Package built using R-devel version 3.3.0.
R Dependecy updated to R (>= 3.3.0) in preparation for next Bioconductor release.

Version 0.99.3

Codes:

All comments removed.
' \n' are removed at end of messages, or the space before '\n' are removed.

Version 1.1.1

Codes:

Added “maxmean” statistics.
Added “wilcoxTest” for Mann-Whitney-U tests for single gene analysis.
Default for GSALight() is now “maxmean” with restandardization.
Fix some issues to make GSALight() equivalent to GSA of Efron and Tibshirani.
The target gene list is now a list instead of a data table.
The Vignette now contains a comprehensive user guide.
All documentations are updated accordingly.

Version 1.1.2

Added “importFrom("stats", "p.adjust", "rbinom", "var", "wilcox.test”)” to NAMESPACE
Import “stats” in description
Added back manual for “wilcoxTest”

Version 1.1.3 and 1.1.4

Bioconductor version updates.

Version 1.1.5

Updated references and manual and vignette.
Added Github URL.

Version 1.1.6

Fixed default settings of permTestLight() by adding match.args and setting nperm=NULL.