Package: geneXtendeR 1.31.0

Bohdan Khomtchouk

geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

Authors:Bohdan Khomtchouk [aut, cre], William Koehler [aut]

geneXtendeR_1.31.0.tar.gz
geneXtendeR_1.31.0.zip(r-4.5)geneXtendeR_1.31.0.zip(r-4.4)geneXtendeR_1.31.0.zip(r-4.3)
geneXtendeR_1.31.0.tgz(r-4.4-arm64)geneXtendeR_1.31.0.tgz(r-4.4-x86_64)geneXtendeR_1.31.0.tgz(r-4.3-arm64)geneXtendeR_1.31.0.tgz(r-4.3-x86_64)
geneXtendeR_1.31.0.tar.gz(r-4.5-noble)geneXtendeR_1.31.0.tar.gz(r-4.4-noble)
geneXtendeR_1.31.0.tgz(r-4.4-emscripten)geneXtendeR_1.31.0.tgz(r-4.3-emscripten)
geneXtendeR.pdf |geneXtendeR.html✨
geneXtendeR/json (API)

Peer review:

Bug tracker:https://github.com/bohdan-khomtchouk/genextender/issues

On BioConductor:geneXtendeR-1.31.0(bioc 3.20)geneXtendeR-1.30.0(bioc 3.19)

bioconductor-package

19 exports 0.82 score 108 dependencies

Last updated 2 months agofrom:0558d4de46

Exports:allPeakLengthsannotateannotate_nbarChartcumlinePlotdiffGOdistinctgene_annotategene_lookuphotspotPlotlinePlotmakeNetworkmakeWordCloudmeanPeakLengthmeanPeakLengthPlotpeakLengthBoxplotpeaksInputpeaksMergeplotWordFreq

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiocStyleBiostringsbitbit64bitopsblobbookdownbslibcachemclicodetoolscpp11crayoncurldata.tableDBIDelayedArraydigestdplyrevaluatefansifastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesglueGO.dbhighrhtmltoolshtmlwidgetshttrigraphIRangesjquerylibjsonliteKEGGRESTknitrlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimenetworkD3NLPopensslorg.Rn.eg.dbpillarpkgconfigplogrpngR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassslamsnowSnowballCSparseArraySummarizedExperimentsystibbletidyselecttinytextmUCSC.utilsutf8vctrswithrwordcloudxfunXMLxml2XVectoryamlzlibbioc