Package: primirTSS 1.25.0

Pumin Li

primirTSS: Prediction of pri-miRNA Transcription Start Site

A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

Authors:Pumin Li [aut, cre], Qi Xu [aut], Jie Li [aut], Jin Wang [aut]

primirTSS_1.25.0.tar.gz
primirTSS_1.25.0.zip(r-4.5)primirTSS_1.25.0.zip(r-4.4)primirTSS_1.25.0.zip(r-4.3)
primirTSS_1.25.0.tgz(r-4.5-any)primirTSS_1.25.0.tgz(r-4.4-any)primirTSS_1.25.0.tgz(r-4.3-any)
primirTSS_1.25.0.tar.gz(r-4.5-noble)primirTSS_1.25.0.tar.gz(r-4.4-noble)
primirTSS_1.25.0.tgz(r-4.4-emscripten)
primirTSS.pdf |primirTSS.html✨
primirTSS/json (API)
NEWS

# Install 'primirTSS' in R:
install.packages('primirTSS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ipumin/primirtss/issues

On BioConductor:primirTSS-1.25.0(bioc 3.21)primirTSS-1.24.0(bioc 3.20)

immunooncologysequencingrnaseqgeneticspreprocessingtranscriptiongeneregulation

4.48 score 2 scripts 219 downloads 6 exports 186 dependencies

Last updated 5 months agofrom:dcff06d171. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 28 2025
R-4.5-winWARNINGFeb 28 2025
R-4.5-macWARNINGFeb 28 2025
R-4.5-linuxWARNINGFeb 28 2025
R-4.4-winWARNINGFeb 28 2025
R-4.4-macWARNINGFeb 28 2025
R-4.3-winWARNINGFeb 28 2025
R-4.3-macWARNINGDec 30 2024

Exports:find_tsspeak_joinpeak_mergeplot_primiRNArun_primirTSSapptrans_cor

Dependencies:abindannotateAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomeBSgenome.Hsapiens.UCSC.hg38bslibcachemcaToolscheckmateclicliprclusterCNErcodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestDirichletMultinomialdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGenomicScoresggplot2glueGO.dbgridExtragtablegtoolsGvizh5mreadHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2interpIRangesisobandJASPAR2018jpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslphastCons100way.UCSC.hg38pillarpkgconfigplogrplyrpngpoweRlawpracmaprettyunitsprogresspromisesProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesseqLogoshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml

primirTSS

Rendered fromprimirTSS.Rmdusingknitr::rmarkdownon Feb 28 2025.

Last update: 2018-09-07
Started: 2018-07-27