NEWS

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ORFik 1.23.8

SIGNIFICANT USER-VISIBLE CHANGES

• Implemented a Ribo-seq ORF detector now included
• Added new export functions for bigwig, covRLE

ORFik 1.13.7

SIGNIFICANT USER-VISIBLE CHANGES

• Massive improvement in speed of coveragePerTiling
• Improved p-shifting analysis (also added verbose output)
• Added possible optimization for annotation
• Rewritten vignettes

ORFik 1.7.17

SIGNIFICANT USER-VISIBLE CHANGES

• Added pmapToTranscriptsF, a much faster pmapToTranscripts.
• All of ORFik now supports weights for representing duplicated reads. This will speed up all function related to NGS data a lot.

ORFik 1.7.0

SIGNIFICANT USER-VISIBLE CHANGES

• The ORFik experiment syntax is ready, to simplifiy ORFik usage with big data.

ORFik 1.3.7

SIGNIFICANT USER-VISIBLE CHANGES

• mapToGRanges is now much faster and uses much less memory. A c++ reimplementation of pmapFromTranscripts from GenomicFeatures.

ORFik 1.1.12

SIGNIFICANT USER-VISIBLE CHANGES

• 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.
• The orf finding function now find the longest orf per stop codon if you set longestORF = TRUE in findORFS, findMapORFs and findORFsFasta

ORFik 1.0.0

• 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