NEWS
CNEr 1.12.0
NEW FEATURES
- Add function orgKEGGIds2EntrezIDs to fetch the mapping between KEGG IDs
and Entrez IDs
- Add function makeAxtTracks
- Add function addAncestorGO
CNEr 1.10.0
NEW FEATURES
- Updated CNE class for storing all the information about
running the pipeline.
- Add read.rmMask.GRanges to read RepeatMasker .out file.
- Add read.rmskFasta to read soft repeat masked fasta file.
- Add the distribution plot of axt alignment matches.
- Add the distribution plot of CNE length.
- Add the syntenicDotplot for axt alignment and GRangePairs.
- When readAxt and readBed, seqinfo is kept when available.
- New fixCoordinates function makes the coordinates of Axt alignments
always relative to positive strands.
- Add parallel subAxt for Axt alignment.
- Add the plot of genomic distribution of CNE.
- Add the function to make bed and bigwig files of CNEs.
BUG FIXES
- Instead of an error, an empty GRangePairs is returned when no CNEs
identified.
CNEr 1.8.0
BUG FIXES
- Fix a bug caused by "format" in the blat step.
NEW FEATURES
- Add the pairwise whole genome alignment pipeline
- Add a new class "GRangePairs"
- "Axt" class is now based on "GRangePairs" class.
- readAncora for reading Ancora format CNE files.