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