August 30, 2018

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:49:42
November 14, 2016

update to latest GSTRUCT

Michael Lawrence authored on 14/11/2016 21:54:30
April 5, 2016

adjustments in response to the vals -> filter renaming in GenomicFeatures

Herve Pages authored on 05/04/2016 22:55:27
October 28, 2015

resurrect improvements that we reverted before the April release, expect breakage for a while

Michael Lawrence authored on 28/10/2015 18:51:00
April 14, 2015

Reverted to r101133, along with NAMESPACE fixes

Michael Lawrence authored on 14/04/2015 21:40:44

Recent work towards supporting the new features... will revert back to a stable version immediately...

Michael Lawrence authored on 14/04/2015 21:32:10
August 11, 2014

add codon tally support. No vbump yet

Gabriel Becker authored on 11/08/2014 23:42:48
May 13, 2014

update to new bam_tally with support for XS counting, which we now support via BamTallyParam@count_xs.

Michael Lawrence authored on 13/05/2014 02:04:05
April 2, 2014

update GSTRUCT (bam_tally); add include_soft_clip parameter for counting over soft clips of a given max length (more accurate allele frequency)

Michael Lawrence authored on 02/04/2014 22:03:40
March 10, 2014

TP53 genome is now named by the TxDb package from which the TP53 region was retrieved, so that it is automatically refreshed with annotation changes, and devel and release can coexist.

Michael Lawrence authored on 10/03/2014 23:10:51
February 12, 2014

clip_overlaps should be clip_overlap

Michael Lawrence authored on 12/02/2014 17:13:58
January 14, 2014

vignette improvements

Michael Lawrence authored on 14/01/2014 19:15:01
September 25, 2013

call Rcode{} instead of code{}

Dan Tenenbaum authored on 25/09/2013 20:07:03
September 20, 2013

update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tally

Michael Lawrence authored on 20/09/2013 02:05:42
July 14, 2013

Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.

Michael Lawrence authored on 14/07/2013 00:43:43