USeq Source Code

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

Commit [r134] Maximize Restore History

DefinedRegionDifferentialSeq

* Added internal check to remove edgeR analysis and proceed if the app throws errors.
SamSubsampler
* New app to subsample a sam/bam file after filtering and randomizing. Needed for comparing read coverage graphs.
BisStat
* Added option to export base level log 2 ratio of fraction methylation in T vs C graphs.
* Renamed graph folders to indicate Base or Window level data

Authored by: biotelerock 2013-07-18

Browse code at this revision

Parent: [r133]

Child: [r135]

changed	/trunk/Documentation/USeqDocumentation/applications.html
changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed	/trunk/Source/edu/utah/seq/analysis/BisSeq.java
changed	/trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java
changed	/trunk/Source/edu/utah/seq/analysis/MethylatedBaseObservation.java
added	/trunk/Source/edu/utah/seq/data/SamSubsampler.java
changed	/trunk/Source/util/gen/Gzipper.java
changed	/trunk/build.properties

USeq Source Code

Commit [r134] Maximize Restore History

/trunk/Documentation/USeqDocumentation/applications.html Diff Switch to side-by-side view

/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/BisSeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MethylatedBaseObservation.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/data/SamSubsampler.java Diff Switch to side-by-side view

/trunk/Source/util/gen/Gzipper.java Diff Switch to side-by-side view

/trunk/build.properties Diff Switch to side-by-side view