NEWS

---

mobileRNA 1.9.3

• changed vignette rendering settings.

mobileRNA 1.9.2

• updated mRNA mapping function; silent errors due to bugs and updated in dependencies.
• Updated RNAdifferentialAnalysis() fails at return: object 'groups' not found.

mobileRNA 1.9.1

• added baymobil integration

mobileRNA 1.7.2

mobileRNA 1.7.1

mobileRNA 1.6.2

• Updated ShortStack mobile sRNA integration

mobileRNA 1.6.1

• Added Namespace dependency to DESCRIPTION Imports/Depends entries: ‘Seqinfo’

mobileRNA 1.5.2

mobileRNA 1.4.1

• Updated several functions including RNAfeatures.

mobileRNA 1.0.15

• Fixed typo in mapRNA

mobileRNA 1.0.14

• Fixed inaccuracies in README
• Fixed bug in RNAmergeGenomes

mobileRNA 1.0.13

• Updates citation

mobileRNA 1.0.12

• Updated RNAfeatures and plotRNAfeatures including new parameters to control plotting and representation of genomic features.
• Updated citation

mobileRNA 1.0.11

• Major updated to RNAfeatures. Instead identifies features independently for the genome annotation rather than using preset features.

mobileRNA 1.0.1

• Version bump following Bioconductor updates.
• Improved the RNAfeatures function due discrepancies. Previously, calculated width rather than relative number of features.
• Improved RNAdistribution function, including fixing a small bug, replaced depreciated functioned and improved aesthetic and code structure.
• Introduced new plotting function plotRNAfeatures.

mobileRNA 0.99.23

• Improved RNAfeatures function

mobileRNA 0.99.22

• Fixed issues in RNAimport function

mobileRNA 0.99.20

• Build redo

mobileRNA 0.99.19

• Missing connective in RNAfeatures when using repeats variable.
• Added additional check for RNAsequences methods.

mobileRNA 0.99.17

• Corrected ORCID references for authors

• Amended RNAmobile() to ensure removal of non-zero values
• Improved look of PCA plot
• Corrected documentation issue and code disparage in plotHeatmap(), and improved styling.
• Included calculation of consensus sequence determination option for RNAsequence()

mobileRNA 0.99.15

• Alteration of vignette and README
• Included clean FASTQ files as example data sets
• Updated R data objects
• Updated citation & news files
• Addition of new function called mapRNA()
• Deletion of RNAloci() and RNAmean() functions
• Additional parameters to RNAimport() to support mRNA data importation
• Removed parallel computation in RNAmergeGenomes()
• Improved documentation of functions and removed inconsistencies.

mobileRNA 0.99.14

Previous changes

• Added a NEWS.md file to track changes to the package.
• RNAconsensus() changed to RNAdicercall()
• Alterations to RNAdicercall() algorithm, including tie options, altered default tidy method.
• RNAdicercall() introduced new column "DicerCount" and improved the functionality, specifically the exclude parameter.
• RNAmobile() introduced new parameter, "threshold"
• Improved RNAsequences() selection algorithm to consider a threshold value, and handling ties.
• Improved error calling on functions
• Added RNAdf2e() function
• Improvements to plotSamplePCA() and plotHeatmap()
• Amended RNAmergeAnnotations function to meet requirement
• Removed unnecessary man files for GFF and FASTA files on remote repo
• Fixed bug in RNAdistribution() plot, when sample specific
• Broadened use of RNAattributes() function.
• Updated vignette
• Updated RNAdicercall() to allow any dicer-classification (not constricted to 20-24)
• Converted cat() to message() for user information from functions
• Amended example data
• Amended CITATION and NEWs file
• Altered examples in RNAmergeAnnotations/Genomes functions to prevent examples saving into users directory
• updates inline with bioconductor requirements
• Amended RNAmergeGenomes() and RNAmergeAnnotations()
• Removed lazy loading of package data
• RNAanalysis() changed name to RNAdifferentialAnalysis()