1.5.4

Fixed issue with changed syntax in DESeq2 function calls in devel version of bioconductor.

v1.3.5b

Fixed Github tag for v1.3.5.

Minor changes.

• Fixed a typo in the documentation (thanks Heath O'Brien!)
• buildAllPlotsForGene will now create directories as needed. (thanks Heath O'Brien!)
• Both buildAllPlotsForGene and buildAllPlots will now throw an informative error if the parent directory does not exist.

v1.3.5

(this github tag somehow got mis-placed. See the fixed tag above.)

v1.3.4

v1.3.4:
Minor bugfixes and additions:

• Manual updated to reflect changes in the most recent version of QoRTs: the mergeNovelSplices function now automatically calculates size factors, if size factors are not set explicitly.
• Fixed typos in the manual.
• Bugfix: Basic functionality now works without a GFF file being specified (as per specification)
• Iterated version number to match Bioconductor versioning.
• Added the ability to suppress the creation of a DESeq2 count container object (for advanced users).

v1.1.16

As always, see the JunctionSeq homepage for installation instructions.

Minor bugfixes: (thanks to Warren McGee)

• When making html summary files with "use.multigene.aggregates" genes set to TRUE,
  JunctionSeq will use shortened html file names in order to avoid filename length
  limitations on certain filesystems when there are numerous genes overlapping with
  one another. Aggregate gene names will be truncated to only include the first and
  last member genes iff there are more than 2 member genes, with a "..." in between.
• If minimalImageFilenames is FALSE, then Image files will similarly be renamed. Otherwise
  they will be reduced in size even further, as per the v1.1.10 update. You can
  control the naming of the png files using the options: "minimalImageFilenames",
  "name.files.with.geneID", and "number.plots"
• Fixed a bug in the phenotype table on the HTML index page.

Various minor "quality-of-life" improvements:

• When available, gene names will be included in all tables.
• The main index data table now includes mouseover text describing each column.
• Added additional information to each plot page.
• Added word wrapping to aggregate genes in the main index tables (thanks to Warren McGee).

In addition: Added further test cases to the testSuite:

• Added a legacy version of output from QoRTs v0.3.17, to test backwards-compatibility.
• Added test cases that test the new functionality.
• Added more genes to the "tiny" dataset in the JctSeqData package. This dataset is used in the examples and in the test suite. It now includes 3 "aggregate genes", which are composed of multiple genes that overlap. This allows fast testing of the "use.multigene.aggregates" parameter in the test suite.

v1.1.10

v1.1.10:

• Changed naming scheme for gene-profile plots, to reduce the length of the filenames.
  Some web hosts are not compatible with excessively long image filenames. When the writeHTMLresults parameter is TRUE (the default), JunctionSeq will now default to a shorter naming scheme in which the image files are named
  by number rather than by gene ID. This behavior can be deactivated setting the
  new "minimalImageFilenames" parameter to FALSE.
• Minor adjustments to the vignette.
• JunctionSeq is now built and tested on SL6 in R 3.2.3

v1.1.3

Very minor typographical fixes and clarifications in the vignette.

v1.1.1

JunctionSeq is officially out of beta and accepted into bioconductor! See the JunctionSeq bioconductor page here. Bioconductor only offers JunctionSeq on the development version currently, but you can still install and run JunctionSeq from this (github) site in the meantime.

Changes from the previous version were minor and cosmetic.

v0.99.8

JunctionSeq is now accepted by Bioconductor!

Very minor changes, mostly just fixing typos in the documentation and testing the functionality of the Bioconductor svn server.

The next version will be 1.0.

Installation instructions can be found on the JunctionSeq website: http://hartleys.github.io/JunctionSeq/index.html

v0.99.6

JunctionSeq is now pre-approved by Bioconductor, and will probably be included in the next Bioconductor release.

Minor update:

• Running in verbose mode, readJunctionSeqCounts now reports the number of gene aggregates found, and the total number of genes that belong to them.
• Iterated version number to 0.99.6, to sync with bioconductor submission version numbering.

Installation instructions can be found on the JunctionSeq website: http://hartleys.github.io/JunctionSeq/index.html