 |
Viewdc71e3a
Port change from devel that prevents conflict between cached TP53 genomesMichael Lawrence authored on 10/03/2014 23:32:24 |
|
Viewf3db568
renamed summarizeVariants to variantSummary the which in GsnapParam is now a GenomicRanges instead of a RangesList refactor the show method of BamTallyParam to rely on showAsCellMichael Lawrence authored on 15/07/2013 23:41:54 |
|
View59c3684
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 |
 |
View0dbb11f
Use readDNAStringSet() instead of read.DNAStringSet().Herve Pages authored on 13/05/2013 23:23:36 |
|
View82c0838
import 'exons'Michael Lawrence authored on 30/03/2013 02:36:06 |
|
View2f697ca
Add GmapGenome->DNAStringSet coercion, exports the whole genome sequence. This means export(x, "genome.fasta") should work.Michael Lawrence authored on 27/03/2013 19:11:09 |
|
View248ed95
Export new stuff, bump versionMichael Lawrence authored on 26/03/2013 21:44:37 |
|
View7afec90
drop import of parallel package, as we apparently do not use it?Michael Lawrence authored on 29/09/2012 04:03:09 |
|
View3dd29e4
Export TP53Which()Michael Lawrence authored on 12/09/2012 05:15:05 |
 |
View297de88
*gmapR option name for returning system calls is now "systemCallMode"Cory Barr authored on 11/09/2012 22:12:30 |
|
View1116df9
added capability to overwrite .system via providing a function to options('gmapRSysCall')Cory Barr authored on 11/09/2012 02:32:47 |
|
View9dfa7ad
added patches supplied by GregCory Barr authored on 10/09/2012 22:52:34 |
|
View1e5e275
Fix typo in spliceSites<-Michael Lawrence authored on 07/09/2012 17:05:26 |
|
Viewe35b784
Fix import of getSeqMichael Lawrence authored on 07/09/2012 17:02:06 |
|
View5fdf642
Add a GRangesList spliceSites<- method. Seems like it is working, but more testing is needed.Michael Lawrence authored on 07/09/2012 16:50:04 |