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NEWS
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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