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NEWS
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ORFik 1.0.0
-----------------------
o first release of ORFik - find Open Reading Frames, automatic RiboSeq
footprint shifts, reassignment of Transcription Start Sites with the use of
CageSeq, plethora of gene identity functions from scientific publications
CHANGES IN VERSION 1.1.12
-----------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Remade many function to handle no names correctly, like tile1 will now
work even for GRangesList without names. Documentation is more logical, and
removed coverageByWindow, since GenomicFeatures::coverageByTranscripts now
works correctly.
CHANGES IN VERSION 1.1.12
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o The orf finding function now find the longest orf per stop codon if
you set longestORF = TRUE in findORFS, findMapORFs and findORFsFasta
CHANGES IN VERSION 1.3.7
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o mapToGRanges is now much faster and uses much less memory. A c++
reimplementation of pmapFromTranscripts from GenomicFeatures.
CHANGES IN VERSION 1.7.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o The ORFik experiment syntax is ready, to simplifiy ORFik usage
with big data.
CHANGES IN VERSION 1.7.17
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Added pmapToTranscriptsF, a much faster pmapToTranscripts.
o All of ORFik now supports weights for representing duplicated reads.
This will speed up all function related to NGS data a lot.
CHANGES IN VERSION 1.13.7
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Massive improvement in speed of coveragePerTiling
o Improved p-shifting analysis (also added verbose output)
o Added possible optimization for annotation
o Rewritten vignettes
CHANGES IN VERSION 1.23.8
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Implemented a Ribo-seq ORF detector now included
o Added new export functions for bigwig, covRLE