Package: DuplexDiscovereR 1.1.0
Egor Semenchenko
DuplexDiscovereR: Analysis of the data from RNA duplex probing experiments
DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.
Authors:
DuplexDiscovereR_1.1.0.tar.gz
DuplexDiscovereR_1.1.0.zip(r-4.5)DuplexDiscovereR_1.1.0.zip(r-4.4)
DuplexDiscovereR_1.1.0.tgz(r-4.4-any)
DuplexDiscovereR_1.1.0.tar.gz(r-4.5-noble)DuplexDiscovereR_1.1.0.tar.gz(r-4.4-noble)
DuplexDiscovereR_1.1.0.tgz(r-4.4-emscripten)
DuplexDiscovereR.pdf |DuplexDiscovereR.html✨
DuplexDiscovereR/json (API)
NEWS
# Install 'DuplexDiscovereR' in R: |
install.packages('DuplexDiscovereR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/egors01/duplexdiscoverer/issues
- RNADuplexSampleClustReads - RNA duplex reads of SPLASH, clustered and assigned to duplex groups
- RNADuplexSampleDGs - RNA duplex reads of SPLASH, clustered and collapsed to duplex groups
- RNADuplexSampleGI - RNA duplex reads of SPLASH derived from chimeric alignments
- RNADuplexesGeneCounts - Gene counts on human chromosome 22, embryonic stem cells
- RNADuplexesRawBed - Chimeric reads of SPLASH converted to .bedpe fromat
- RNADuplexesRawChimSTAR - Chimeric reads of SPLASH
- SampleGeneAnnoGR - Gene coordinates on human chromosome 22
- SampleSmallGI - RNA duplex reads of SPLASH derived from chimeric alignments
- SampleSpliceJncGR - Gene coordinates on human chromosome 22
On BioConductor:DuplexDiscovereR-1.1.0(bioc 3.21)DuplexDiscovereR-1.0.0(bioc 3.20)
sequencingtranscriptomicsstructuralpredictionclusteringsplicedalignment
Last updated 2 days agofrom:37477e10cc. Checks:OK: 3 WARNING: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 31 2024 |
R-4.5-win | WARNING | Oct 31 2024 |
R-4.5-linux | OK | Oct 31 2024 |
R-4.4-win | WARNING | Oct 31 2024 |
R-4.4-mac | OK | Oct 31 2024 |
Exports:annotateGIavailableDisplayParsclassifyTwoArmChimerasclusterDuplexGroupscollapse_duplex_groupscollapseIdenticalReadscompareMultipleInteractionscomputeGISelfOverlapsconvert_gi_to_rangesdd_get_chimeric_readsdd_get_chimeric_reads_statsdd_get_duplex_groupsdd_get_reads_classesdd_get_run_statsDuplexDiscovererResultsDuplexTrackget_char_count_cigargetChimericJunctionTypesgetRNAHybridsgetSpliceJunctionChimerasmakeDfFromGimakeGiFromDfrunDuplexDiscoPreprocrunDuplexDiscoverershowwriteGiToSAMfile
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggscigluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc