LOG of the CHANGES in the package Test Version 0.9.4-2: * Fixed a file mismatch in vignette Version 0.9.4: * Cran release Version 0.9.3: * Added the function 'getSequenceFromNCBI()' * Added the function 'coverageDensity()' * import* function deprecated and placed into GenomicTools.fileHandler package Version 0.9.2: * Windows support for file handling improved Version 0.9.1: * Typos in manual fixed * Typos in vignette fixed * Minor bugfixes in 'blastSeq' * Added the function 'importBed()' * output of 'print.fa()' adjusted * Bugfix in 'getFastaFromBed()' - 'version' option wasn't used properly * Improvement in 'exportBed' - If file=NULL (default) the variable name is used as file name * Improvement in 'exportFA' - If file=NULL (default) the variable name is used as file name * Improvements in 'getAnnotation()' - Better guessing of right URL at Ensembl * Improvements in 'getFastaFromBed()' - fasta files are now imported using the 'Rsamtools::scanFa' function * Improvements in 'plotHit()' - Better guessing of right URL at Ensembl - Bam files that are used in groups are now displayed for better control * Improvements in 'summary.fa()' - Output is now better aligned * All connections to NCBI use now 'https' instead of 'http' Version 0.9: * Major update for functionality and usability * Added the authors@R filed to the Description * Added the log option to blastSeq. This way a crashed blast run and continue where it crashed. * Added the nrow option for the 'importGTF' function * Added the 'print.pedMap' function * Added the 'summary.pedMap' function * Added the 'targetScan' function * Added the functions 'subGprobs', 'subPhased' and 'subDose' * Bugfixed the blastSeq function * Bugfixed the importXML function * The 'summary.fa' function is now more informative * Added the 'plotHit' function * Added the 'intersectXMLAnnot' function * Added several small helper functions * Added the 'getfastaFromBed' function * Added the 'exportFA' function * Added the 'exportBed' function * Deprecated the 'importPedMap' function * Added the package Vignette Version 0.1: * Added the data example.fa * importFA returns now an object of class 'fa' instead of 'character' * Added the function 'print.fa' * Added the function 'summary.fa' Version 0.0-2: * Included the function 'getEnsgInfo' * Included the function 'getGeneSeq' * Updated the manual pages * Improved the input checks in the 'blastSeq' function * Included the function 'print.blastRes' * Included the function 'summary.blastRes' * Included the function 'importGFF3' * Added hoardeR to a Git-hub repository Version 0.0-1: * First build with basic functionality