USeq Source Code

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

Source Code Commit Log

Commit	Date
[r187] by biotelerock Added new beta app for annotating vcf variants with splice junction affects.	2013-12-03 22:57:09	Tree
[r186] by tmosbruger Bug Fix	2013-12-03 18:13:50	Tree
[r185] by biotelerock Added ability to set the minimum base read coverage threshold, defaults to 5 alignments	2013-12-02 21:10:53	Tree
[r184] by tmosbruger Added support for David's best practices to TomatoFamer. See 'exome_best'	2013-12-02 15:03:47	Tree
[r183] by biotelerock DefinedRegionDifferentialSeq * Fixed bug when DESeq was outputting FDRs with "NA", these were being assigned the max FDR, switched it to 0. Note, this won't effect most analysis since these genes also have a log2 of 0 and wouldn't survive standard log2Ratio thresholding. NovoalignBisulfiteParser * Fixed a bug in the -b4 novoalignment parsing * Remove support for native novoalign format, just sam/ bam now.	2013-11-27 23:17:56	Tree
[r182] by biotelerock Updates to bisulfite processing to support -b4 novoalignments, reinstatement of overlapping paired read collapsing, additions to VCF classes to allow for scoring splice junction effects.	2013-11-20 18:07:08	Tree
[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

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