USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Source Code Commit Log

Commit	Date
[r181] by biotelerock Updates to the docs with current best practices.	2013-11-20 18:05:30	Tree
[r180] by biotelerock Added some test sequence files with examples for running through the MaxEntScan apps.	2013-11-08 23:43:51	Tree
[r179] by biotelerock Updated with latest changes	2013-11-08 23:33:45	Tree
[r178] by biotelerock Added Java implementations of Yeo and Burge's Max Ent Scan algorithms for human splice site detection	2013-11-08 23:33:19	Tree
[r177] by tmosbruger VCFAnnotator: This app now supports VAAST 2.0 output, including InDels	2013-11-06 21:51:37	Tree
[r176] by biotelerock SRAProcessor * Added option to set quality score offset to 64, needed for some Illumina datasets MiRNACorrelator * Added ggplot2 box whisker plot functionality	2013-11-06 21:17:25	Tree
[r175] by tmosbruger TomatoFarmer: Implement deleteing intermediate bams TFCommandExomeVariant: Fixed chunking behavior when inverval exactly matches remaining chunk space. This produced a zero length interval, which GATK dislikes.	2013-11-06 15:45:06	Tree
[r174] by biotelerock Updated docs for chIPSeq and RNASeq.	2013-11-04 23:47:24	Tree
[r173] by tmosbruger MultiSampleVCFFilter: Allow strict genotype matching, which drops records with missing genotypes.	2013-11-04 20:36:50	Tree
[r172] by biotelerock DefinedRegionDifferentialSeq * Added a System.setProperty("java.awt.headless", "true") to allow running app in non x11 mode. VCFSample * Changed how it recognizes a no call to anything that starts with ./. so these are skipped FilterIntersectingRegions * Added option to split gtf/ gff files	2013-11-04 20:32:34	Tree

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