Package: broadSeq 0.99.3
broadSeq: broadSeq : for streamlined exploration of RNA-seq data
This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.
Authors:
broadSeq_0.99.3.tar.gz
broadSeq_0.99.3.zip(r-4.5)broadSeq_0.99.3.zip(r-4.4)broadSeq_0.99.3.zip(r-4.3)
broadSeq_0.99.3.tgz(r-4.4-any)broadSeq_0.99.3.tgz(r-4.3-any)
broadSeq_0.99.3.tar.gz(r-4.5-noble)broadSeq_0.99.3.tar.gz(r-4.4-noble)
broadSeq.pdf |broadSeq.html✨
broadSeq/json (API)
NEWS
# Install 'broadSeq' in R: |
install.packages('broadSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dasroy/broadseq/issues
On BioConductor:broadSeq-0.99.3(bioc 3.20)
Last updated 1 months agofrom:788035bc21
Exports:assay_plotbiplotAnyPCcombinedEnrichmentgenes_plotgetFeatureLoadRankingnormalizeEdgerCPMplot_MDSplotAnyPCplotHeatmapClusterprcompTidyround_dfsampleAssay_plottransformDESeq2use_DELocaluse_deseq2use_EBSequse_edgeRuse_edgeR_exactuse_edgeR_GLMuse_limmause_limma_trenduse_limma_voomuse_multDEuse_NOIseqvolcanoPlot
Dependencies:abindannotateAnnotationDbiapeaplotaskpassbackportsbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiocStyleBiostringsbitbit64bitopsblobblockmodelingbookdownbootbriobroombslibcacachemcallrcarcarDatacaToolscirclizecliclueclusterclusterProfilercodetoolscolorspaceComplexHeatmapcorrplotcowplotcpp11crayoncurldata.tableDBIDelayedArrayDELocaldescDESeq2diffobjdigestdoParallelDOSEdownloaderdplyrEBSeqedgeRenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsgclusgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggforceggfunggnewscaleggplot2ggplotifyggpubrggraphggrepelggsciggsignifggtreeGlobalOptionsglueGO.dbGOSemSimgplotsgraphlayoutsgridExtragridGraphicsgsongtablegtoolsHDO.dbhighrhtmltoolshttrigraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptrnnetNOISeqnumDerivopensslpatchworkpbkrtestpermutepheatmappillarpkgbuildpkgconfigpkgloadplogrplyrpngpolyclippolynompraiseprocessxpspurrrqapquantregqvalueR6randomcoloRrappdirsRColorBrewerRcppRcppArmadilloRcppEigenregistryrematch2reshape2rjsonrlangrmarkdownrprojrootRSQLiterstatixRtsneS4ArraysS4VectorssassscalesscatterpiesechmseriationshadowtextshapesnowSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattibbletidygraphtidyrtidyselecttidytreetinytextreeioTSPtweenrUCSC.utilsutf8V8vctrsveganviridisviridisLitewaldowithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc