Source Code Log


Commit Date  
[r167] by biotelerock

Latest comments

2013-10-15 16:25:48 Tree
[r166] by biotelerock

Added catch to rename broken useq archives so these are skipped in subsequent autoconversion

2013-10-15 16:24:37 Tree
[r165] by biotelerock

Added catch for fetching last bases from an array of regions

2013-10-15 16:23:29 Tree
[r164] by biotelerock

Updated apps to work with kingspeak cluster and use rsync for all transfers

2013-10-15 16:23:13 Tree
[r163] by biotelerock

Added catch for fetching last bases from an array of regions

2013-10-15 16:22:32 Tree
[r162] by biotelerock

Added debugging info to parsing output

2013-10-15 16:21:34 Tree
[r161] by biotelerock

Removed a requirement that non paired analysis contain matching t vc samples

2013-10-15 16:20:03 Tree
[r160] by biotelerock

Removed a requirement that non paired analysis contain matching t vc samples

2013-10-15 16:19:49 Tree
[r159] by biotelerock

Bug fix to block genes with excessive counts from deseq analysis

2013-10-15 16:19:25 Tree
[r158] by biotelerock

Mods for new apps

2013-10-15 16:18:32 Tree
[r157] by biotelerock

New app for associating miRNA expression with target gene expression values

2013-10-15 16:16:58 Tree
[r156] by tmosbruger

Bunch of edits to TomatoFarmer

2013-09-30 23:05:10 Tree
[r155] by monkeymanstan

1. Fixed alignments params for small RNAs to allow for >1 mismatch, including homopolymer filtering.
2. Now specifying small RNA read adapter from sequencing report, not the one reported on the sequencing Bioinfo wiki

2013-09-17 21:32:13 Tree
[r154] by biotelerock

Removed some debugging statements from STP

Corrected a bug that was causing USeq2UCSCBig to error out when working with stranded bed files in some cases.

2013-09-12 19:49:43 Tree
[r153] by biotelerock

ExportExons
* Added name score and strand to the output
DefinedRegionDifferentialSeq
* Fixed a bug where genes with excessive counts were still being included in the DESeq analysis
USeq2UCSCBig
* Added a sandbox to the UCSC executables to limit memory and time on linux systems

2013-09-11 21:58:51 Tree
[r152] by biotelerock

Fixed issue when running a no replica analysis that caused DESeq to error out.

2013-09-05 18:15:10 Tree
[r151] by biotelerock

updated to USeq_8.6.6

2013-09-05 16:55:51 Tree
[r150] by biotelerock

Merged docs with Tim's DRDS bug fix

2013-09-05 15:12:53 Tree
[r149] by biotelerock

Modified output to a table instead of multi line

2013-09-05 15:06:19 Tree
[r148] by biotelerock

Switched flag back to deleting temp files

2013-09-05 15:05:35 Tree
[r147] by tmosbruger

DRDS fix added

2013-09-04 15:14:46 Tree
[r146] by tmosbruger

Fixed an error where improperly paired reads and stacked pairs weren't counted towards the gene's read count.

2013-09-04 15:09:14 Tree
[r145] by biotelerock

Misc mods, nothing significant

2013-08-30 22:22:29 Tree
[r144] by biotelerock

Updated with poi classes

2013-08-30 22:21:38 Tree
[r143] by monkeymanstan

Initial commit of CassetteOptimizer and associated classes

2013-08-23 20:22:59 Tree
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