NEWS

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AssessORF 1.7.1 (2020-10-23)

• Genome viewer plots will now show the forward strand above the reverse strand, and reading frames will now be laid out in 1 through 6 order moving down the genome viewer (before it was reversed)

AssessORF 1.7.0 (2020-10-21)

• Can now toggle interactivity of the genome viewer when plotting Assessment objects
• Can now zoom into an initial range with the genome viewer when plotting Assessment objects
• Documented the genome viewer in the plot.Assessment man page
• Added a genome viewer example to the vignette
• Fixed a bug that was causing an error when users attempted to zoom out ten-fold with the genome viewer plot # AssessORF 1.3

AssessORF 1.3.1 (2019-10-22)

• Data for six new strains, S. pyogenes AP1, E. coli BW25113, S. aureus HG001, L. lactis MG1363, B. subtilis NCIB 3610, and L. monocytogenes 10403S, have been added to AssessORFData
• CITATION file added as corresponding paper has now been published
• Updated MapAssessmentData such that verbose output is cleaner and more informative # AssessORF 1.1

AssessORF 1.1.7 (2019-04-29)

• Added a function, CompareAssessmentResults, for comparing two results objects against each other
• Added a processors parameter to MapAssessmentData for compatibility with DECIPHER functions

AssessORF 1.1.6 (2019-04-07)

• Added parameters to AssessGenes to bound the range in which to look for conserved starts that can serve as alternative options to a predicted start
• Added a parameter to AssessGenes that requires ORFs with protein evidence but no predicted start to have a certain minimum number of peptide hits in order to be included in the final output

AssessORF 1.1.5 (2019-01-11)

• Update to how conserved starts and conserved stops are utilized in AssessGenes
• Removed weighted score
• Made clarifications to the man pages
• Minor edits to the vignette

AssessORF 1.1.4 (2018-12-15)

• Updated AssessGenes to make sure predicted stops are valid for their corresponding genes, and users will be warned appropriately if a predicted stop is invalid
• Minor updates to plots
• Bug fixes on previous version's MapAssessmentData updates

AssessORF 1.1.3 (2018-11-12)

• Fixed a bug affecting coverage related to gaps in alignments in MapAssessmentData
• Used exponential moving averages to filter out bad alignment regions in MapAssessmentData

AssessORF 1.1.2

• Implemented a fix to the vignette so it builds without an internet connection

AssessORF 1.1.1

• Reduced time it takes to run MapAssessmentData examples # AssessORF 0.99

AssessORF 0.99.22

• Added data package to Suggests list
• Tweaked connection to data package in the AssessGenes function

AssessORF 0.99.21

• Minor edits to man pages and the vignette

AssessORF 0.99.20

• Minor edits to man pages and the vignette

AssessORF 0.99.19

• NEWS file added