| 036206e1 |
CHANGES IN VERSION 1.21.1
-------------------------
BUG FIXES
o Fixed ENSEMBL host for rnorvegicus_gene_ensembl. Using default host now instead of may2012.archive.ensembl.org.
|
| 9d24b30c |
CHANGES IN VERSION 1.14.2
-------------------------
BUG FIXES
o Corrected format check for experiment.table: Spaces are not excepted any longer, because they lead to downstream errors.
|
| 606ba102 |
CHANGES IN VERSION 1.14.1
-------------------------
BUG FIXES
o Compatibility update: Replaced class() checks with is().
|
| f037158d |
CHANGES IN VERSION 1.13.1
|
| 84010fb3 |
-------------------------
BUG FIXES
o Compatibility update: Replaced deprecated fetchExtendedChromInfoFromUCSC() with getChromInfoFromUCSC().
|
| 9bda87f5 |
CHANGES IN VERSION 1.11.1
-------------------------
BUGFIXES
o Bugfix for error when exporting empty peaks in univariateHMM.
|
| ff7f40fe |
CHANGES IN VERSION 1.9.2
------------------------
BUGFIXES
o Bugfix for error when exporting empty peak lists.
|
| 0bd289b0 |
CHANGES IN VERSION 1.7.2
------------------------
BUGFIXES
o Compatibility fixes for the new release of ggplot2 (3.0.0).
o seqlevels() that are smaller than binsize are dropped properly in fixedWidthBins() and variableWidthBins().
|
| f696a25d |
CHANGES IN VERSION 1.5.3
------------------------
SIGNIFICANT USER-LEVEL CHANGES
o Function 'changePostCutoff()' works on univariate peak calls without posterior needing to be present.
|
| 46810a96 |
CHANGES IN VERSION 1.5.1
|
| acc0f37d |
------------------------
SIGNIFICANT USER-LEVEL CHANGES
|
| 8f4f5e80 |
o New column 'maxPostInPeak' containing the maximum posterior within each peak.
o Score in exported BED files is calculated as -10*log10(maxPostInPeak).
|
| 2274651a |
|
| 0dbcedb9 |
o 'changeFDR()' was renamed to 'changeMaxPostCutoff()'.
|
| acc0f37d |
|
| 19149077 |
CHANGES IN VERSION 1.3.1
|
| f4accf0f |
------------------------
NEW FEATURES
o New parameter 'stepsize' allows sliding bins. This improves localization of peaks.
SIGNIFICANT USER-LEVEL CHANGES
|
| 6304757d |
o New default value for Chromstar(..., stepsize = 1/2 * binsize).
|
| f4accf0f |
|
| b5d97964 |
CHANGES IN VERSION 1.1.4
|
| cce1d434 |
------------------------
BUG FIXES
o Fixed a mistake in the calculation of differential scores from version 1.1.2
|
| f4accf0f |
|
| cce1d434 |
|
| f67f0b54 |
CHANGES IN VERSION 1.1.2
------------------------
NEW FEATURES
o Proper print() methods for all objects.
|
| b73475f8 |
BUG FIXES
|
| cce1d434 |
o Fixed a bug where chromosomes with a single bin were making problems.
|
| b73475f8 |
|
| f67f0b54 |
|
| 1dbc900e |
CHANGES IN VERSION 1.1.1
------------------------
NEW FEATURES
o Selection of peaks can be done with 'changeFDR'.
o Peak calls are available in each chromstaR-object as list entry '$peaks'.
SIGNIFICANT USER-LEVEL CHANGES
o 'plotFoldEnrichment' renamed to 'plotEnrichment'.
o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates' replaced by 'exportCounts', 'exportPeaks', 'exportCombinations'.
BUG FIXES
o Proper computation of fold enrichments, with < 1 indicating depletion and > 1 indicating enrichment.
DEPRECATED AND DEFUNCT
o 'changePostCutoff'.
o 'plotFoldEnrichment'.
o 'exportBinnedData', 'exportUnivariates', 'exportMultivariates', 'exportCombinedMultivariates'.
|
