USeq Source Code

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

Commit [r232] Maximize Restore History

Lots of clean up.

Updated DRDS to DESeq2: major changes, different dispersion fit, different log2Rto calculation, automatic independence filtering. All results in more diff expressed genes compared to the older depreciated methods. Old diff genes are pretty much a subset of new diff genes.

Authored by: biotelerock 2014-05-02

Browse code at this revision

Parent: [r231]

Child: [r233]

changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed	/trunk/Source/edu/expr/MiRNACorrelator.java
changed	/trunk/Source/edu/utah/seq/analysis/DefinedRegionDifferentialSeq.java
changed	/trunk/Source/edu/utah/seq/analysis/DefinedRegionRNAEditing.java
removed	/trunk/Source/edu/utah/seq/analysis/MultipleReplicaDefinedRegionScanSeqs.java
changed	/trunk/Source/edu/utah/seq/analysis/MultipleReplicaScanSeqs.java
changed	/trunk/Source/edu/utah/seq/analysis/OverdispersedRegionScanSeqs.java
changed	/trunk/Source/edu/utah/seq/analysis/RNAEditingScanSeqs.java
changed	/trunk/Source/edu/utah/seq/analysis/RNASeq.java
changed	/trunk/Source/edu/utah/seq/analysis/multi/PairedCondition.java
changed	/trunk/Source/edu/utah/seq/data/HeatMapMakerPosNeg.java
changed	/trunk/Source/edu/utah/seq/useq/apps/Bar2USeq.java

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

/trunk/Source/edu/expr/MiRNACorrelator.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/DefinedRegionRNAEditing.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MultipleReplicaDefinedRegionScanSeqs.java

File was removed.

USeq Source Code

Commit [r232] Maximize Restore History

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

/trunk/Source/edu/expr/MiRNACorrelator.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/DefinedRegionRNAEditing.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/analysis/MultipleReplicaDefinedRegionScanSeqs.java

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

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

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

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

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

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

/trunk/Source/edu/utah/seq/useq/apps/Bar2USeq.java Diff Switch to side-by-side view