Package: DNAfusion 1.7.0

Christoffer Trier Maansson

DNAfusion: Identification of gene fusions using paired-end sequencing

DNAfusion can identify gene fusions such as EML4-ALK based on paired-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK-specific but not EML4-specific probes.

Authors:Christoffer Trier Maansson [aut, cre], Emma Roger Andersen [ctb, rev], Maiken Parm Ulhoi [dtc], Peter Meldgaard [dtc], Boe Sandahl Sorensen [rev, fnd]

DNAfusion_1.7.0.tar.gz
DNAfusion_1.7.0.zip(r-4.5)DNAfusion_1.7.0.zip(r-4.4)DNAfusion_1.7.0.zip(r-4.3)
DNAfusion_1.7.0.tgz(r-4.4-any)DNAfusion_1.7.0.tgz(r-4.3-any)
DNAfusion_1.7.0.tar.gz(r-4.5-noble)DNAfusion_1.7.0.tar.gz(r-4.4-noble)
DNAfusion_1.7.0.tgz(r-4.4-emscripten)DNAfusion_1.7.0.tgz(r-4.3-emscripten)
DNAfusion.pdf |DNAfusion.html✨
DNAfusion/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/ctriermaansson/dnafusion/issues

On BioConductor:DNAfusion-1.7.0(bioc 3.20)DNAfusion-1.6.0(bioc 3.19)

bioconductor-package

8 exports 0.36 score 72 dependencies

Last updated 2 months agofrom:ee3b533da8

Exports:ALK_sequencebreak_positionbreak_position_depthEML4_ALK_analysisEML4_ALK_detectionEML4_sequencefind_variantsintrons_ALK_EML4

Dependencies:abindAnnotationDbiaskpassbamsignalsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysTxDb.Hsapiens.UCSC.hg38.knownGeneUCSC.utilsvctrsXMLXVectoryamlzlibbioc