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Bioconductor Changlog.
Thu, 02 Jul 2009
rtracklayer
The error handler in the HTML parser now allows for an empty 'level' argument.
Support coercion of first argument in GenomicData. Rename 'chrom' to
'space' for data frame objects.
Tweak demo and vignette.
Ensure scores are numeric in BED output.
rtracklayer
Updating the version number for dependency IRanges.
Reverted a change to score method for RangedData objects.
Updated the cpneTrack data object to the new Sequence framework.
Fixed a bug in score extraction in RangedData objects when score is NULL.
rtracklayer
Version bump.
Note about scores being 1 based.
Smarter automatic coercion to UCSC chromosome IDs.
Check for NAs and out of range values in exported BED scores.
rtracklayer
More fixes for XDataFrame -> DataFrame.
Import DataFrame, not XDataFrame. Update IRanges dependency, bump version.
rtracklayer
Version bump.
Transform block starts from 0 based to 1 based.
Fix bug when setting the range on a UCSCSession.
rtracklayer
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
rtracklayer
Fix for UCSC now requiring the table name to be specified during table queries.
rtracklayer
Fix minor doc problems.
rtracklayer
Fix cpneTrack.rda for changes in TypedList structure.
GFF3 intervals now treated as half-open (spec was not clear)
rtracklayer
Fix cpneTrack.rda for changes in IRanges.
rtracklayer
Remove browserView() generic arg defaults.
rtracklayer
Remove browserView() generic arg defaults.
Make imagewidth a parameter to browserView() instead of weird option.
Respect BioC/rtracklayer/imagewidth option for setting the image width
in the UCSC browser. Other various tweaks.
rtracklayer
bumped version number
Update UCSCData show method for changes in IRanges.
rtracklayer
Update UCSCData show method for changes in IRanges.
Doc-related updates.
Export visible methods.
rtracklayer
Depend on IRanges 1.1.34.
Documentation fixes.
Add visible and visible<- accessors for a simple way to show/hide
tracks in a browser view.
Add microRNA targets dataset and demo (for paper)
Take in the genome-themed RangedData (track) wrappers from BSgenome.
rtracklayer
Version bump.
Normalize sequence names to conform with UCSC conventions.
rtracklayer
Documentation, version bump, NAMESPACE updates.
Add new framework for downloading UCSC tables/tracks based on
UCSCTableQuery class.
Add blocks() function for getting the blocks (exons) out of RangedData
objects imported from BED.
Add $ and $<- as aliases for track() and track<-()
Merge '*' zooming method on RangesList to IRanges.
rtracklayer
Update cpneTrack.rda for new class structure.
Suggest version 1.1.1 of microRNA.
Depend on BSgenome 1.11.5.
rtracklayer
Depend on BSgenome 1.11.5.
Fix lack of quotes around track<- in do.call.
Add version-specific deps on Biostrings, BSgenome and IRanges. Bump version.
Disable annoying trackline string length/char warnings. Much too
strict. Also import rbind method from IRanges to fix WIG import.
rtracklayer
Refactor 'layTrack' into 'track<-', replacement method has a much
nicer syntax. Also add [[ and [[<- as aliases for 'track' and
'track<-', respectively. Fix up some documentation issues.
rtracklayer
Add TODO list.
Massive move to IRanges infrastructure. Testing not yet
complete. Also, greatly improved interface to UCSC table browser
(i.e. their database).
rtracklayer
Remove largely untested and certainly unused Argo backend. Not worth
the maintenance.
Clean up depends, imports and suggests. More to come.
rtracklayer
Import only needed parts of IRanges and Biostrings (and Biostrings is
on its way out of the imports altogether), rather than attaching them.
This avoids lots of name conflicts in the user's workspace.
Fix xpath and error handling for XML >= 1.98-0, which is now the minimum required version.
Fix BED import without scores.
rtracklayer
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
rtracklayer
Attempt to fix Biostrings example in the vignette.
rtracklayer
Add suggests on microRNA.
rtracklayer
Allow curl options to be passed to the ucscSession constructor. Allows
circumventing proxies, for example.
Remove require(Biostrings) call. Fix the vignette.
rtracklayer
Bump version, update maintainer email address.
rtracklayer
minor mods to reflect changes in Biostrings
rtracklayer
Bump version to 1.1.17.
Remove hsTargets.rda and documentation, as that was only for the BioC08
tutorial. Start converting the start/end field to integer, rather than
numeric. Fix bug in URL encoding of GFF output. Fix range calculation
in scaling of genomeSegment objects. Improve efficiency of BED parsing
when there is no track line. Add exercises to vignette.
rtracklayer
Added humanStemCell package to the Suggests field.
rtracklayer
Added humanStemCell package to the Suggests field.
rtracklayer
Minor edit to vignette to reflect addition of hsTargets data set.
Moved hsTargets data into rtracklayer package.
Bump version.
Make browserView() tend to generate shorter URLs so that things work
most of the time on Windows, where there seems to be some URL length
limit. Make [ method on ucscTrackModes return an instance of
ucscTrackModes, rather than a character vector.
Also remove stray browser().
Various bug fixes, add cpneTrack demo track, better vignette.
rtracklayer
Begin rewriting the vignette, start cleaning up ucscTrackModes mess.
rtracklayer
Hopefully fix issues with XML package. Hopefully next version of XML
will be compatible. Also remove stray browser().
Fix many more bugs related to track importing (all formats) and exporting in the
UCSC format.
rtracklayer
Fix doc of trackSet method on ucscSession class (removed format parameter).
Fix uploading wig tracks with only one strand.
Pass R CMD check without warnings. Fix many bugs. Hopefully will work
now for Vince. Documentation probably still needs some work.
rtracklayer
Bump version (remove date field).
rtracklayer
Bump version (remove date field).
Fix various import bugs so that examples run.
* Don't even try to split up WIG tracks by strand when some strand
values are missing.
* Fix setting BED import start positions
* Don't assume that every feature in GFF3 has an ID attribute. If even
one is missing, don't use as rownames.
rtracklayer
Use better names for the tracks resulting from the strand split when exporting WIG.
rtracklayer
Fix some bugs in the GFF parser. Also update vignette for new API.
Add some development notes.
Major update - many bug fixes and improvements.