Package: lncRna 1.1.0

Jan Pawel Jastrzebski

lncRna: A Comprehensive Workflow for Long Non-coding RNA Identification and Functional Analysis

Provides a complete workflow for the identification, analysis, and functional annotation of long non-coding RNAs (lncRNAs) from RNA-Seq data. The package includes functions for filtering transcripts from GTF files, evaluating the performance of multiple coding potential prediction tools (e.g., CPC2, PLEK, CPAT), and summarizing their agreement. It enables systematic performance analysis of individual tools, "at least N" tool consensus, and all possible tool combinations. Functional analysis is supported through the identification of potential cis- and trans-acting interactions with protein-coding genes, followed by enrichment analysis. Results can be visualized using a variety of plots, including radar plots, clock plots, and interactive Sankey diagrams.

Authors:Jan Pawel Jastrzebski [aut, cre], Damian Czopek [ctb, aut], Mariusz Jankowski [ctb], Monika Gawronska [ctb], Wiktor Babis [ctb], Stefano Pascarella [ctb], Hugo Gruson [ctb]

lncRna_1.1.0.tar.gz
lncRna_1.1.0.zip(r-4.7)lncRna_1.1.0.zip(r-4.6)lncRna_1.1.0.zip(r-4.5)
lncRna_1.1.0.tgz(r-4.6-any)lncRna_1.1.0.tgz(r-4.5-any)
lncRna_1.1.0.tar.gz(r-4.7-any)lncRna_1.1.0.tar.gz(r-4.6-any)
lncRna_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
lncRna/json (API)
NEWS

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

Bug tracker:https://github.com/prodakt/lncrna/issues

On BioConductor:lncRna-1.1.0(bioc 3.24)lncRna-1.0.0(bioc 3.23)

softwaregeneexpressionrnaseqtranscriptionvisualizationqualitycontrolfunctionalgenomicsclassificationfunctionalprediction

5.98 score 8 stars 10 scripts 72 downloads 18 exports 85 dependencies

Last updated from:ae94230cbb. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE188
linux-devel-x86_64OK243
source / vignettesOK258
linux-release-x86_64OK282
macos-release-arm64OK157
macos-oldrel-arm64OK143
windows-develOK158
windows-releaseOK151
windows-oldrelOK159
wasm-releaseOK160

Exports:aggregateCodPotannotateInteractionsbestToolbestToolAtleastbestToolCombinationcalculateCMcreateTrainTestSetsevaluateToolCombinationsevaluateToolsThresholdsfindCisInteractionsfindTransInteractionsgetBiotypesgetGtfStatsplotClockMetricsplotRadarMetricsplotSankeyInteractionsplotVennCodPotprepareEvaluationSets

Dependencies:askpassbackportsbase64encBiocGenericsbslibcachemcheckmatecliclustercolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfmsbfontawesomeforeignFormulafsgenericsGenomicRangesggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimennetopensslotelpatchworkpillarpkgconfigplotlyPolychromepromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownrpartrstudioapiS4VectorsS7sassscalesscatterplot3dSeqinfostringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

lncRna: A Comprehensive Pipeline for lncRNA Identification and Functional Analysis

Jan Pawel Jastrzebski, Damian Czopek, Mariusz Jankowski, Stefano Pascarella, Wiktor Babis, Monika Gawronska

Rendered fromlncRna.Rmdusingknitr::rmarkdownon Jun 05 2026.

Last update: 2026-03-11
Started: 2025-12-17