CHANGES IN VERSION 1.3.3 ------------------------- NEW FEATURES o STAR fusion import function: importFusionData o STAR run function: starInstallation o STAR installation function: starRun o BiocParallel supported functions: STAR import fusionName supportingReads filterList CHANGES IN VERSION 1.3.9 ------------------------- NEW FEATURES o Rsubread aligner is used instead of tophat. CHANGES IN VERSION 1.3.12 -------------------------- NEW FEATURES o Picard-tools can be downloaded in chimara folder, picardInstallation. o The wrapper function validateSamFile uses picard tools to validate SAM/BAM files. o The wrapper function filterSamReads allows SAM and BAM filtering. CHANGES IN VERSION 1.3.15 ------------------------- NEW FEATURES o GapFiller Nadalin et al BMC Bioinformatics was implemented as de novo validation tool for fusion break point. CHANGES IN VERSION 1.5.2 ------------------------- NEW FEATURES o prettyPrint function was added to generate a table delimited file output form a list of fSet objects. o oncofuse annotation was added. CHANGES IN VERSION 1.7.1 ------------------------- NEW FEATURES o Fusions data generated by Rsubread can be imported. CHANGES IN VERSION 1.7.10 ------------------------- NEW FEATURES o Fusions data generated by fusionCatcher can be imported. CHANGES IN VERSION 1.9.2 ------------------------- NEW FEATURES o Fusions data generated by tophat-fusion-post can be imported. o Star import function was improved. o Annotation of fusion is more robust as it it is clearly linked to specific genomic releases. e.g. h19 uses BSgenome.Hsapiens.UCSC.hg19 and TxDb.Hsapiens.UCSC.hg19.knownGene