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✨
DESCRIPTION |NEWS
card.svg |card.png
lncRna/json (API)

# 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)

software geneexpression rnaseq transcription visualization qualitycontrol functionalgenomics classification functionalprediction

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

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

Target	Result	Time
bioc-checks	NOTE	188
linux-devel-x86_64	OK	243
source / vignettes	OK	258
linux-release-x86_64	OK	282
macos-release-arm64	OK	157
macos-oldrel-arm64	OK	143
windows-devel	OK	158
windows-release	OK	151
windows-oldrel	OK	159
wasm-release	OK	160

Exports:aggregateCodPot annotateInteractions bestTool bestToolAtleast bestToolCombination calculateCM createTrainTestSets evaluateToolCombinations evaluateToolsThresholds findCisInteractions findTransInteractions getBiotypes getGtfStats plotClockMetrics plotRadarMetrics plotSankeyInteractions plotVennCodPot prepareEvaluationSets

Dependencies:askpass backports base64enc BiocGenerics bslib cachem checkmate cli cluster colorspace cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fmsb fontawesome foreign Formula fs generics GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr memoise mime nnet openssl otel patchwork pillar pkgconfig plotly Polychrome promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rpart rstudioapi S4Vectors S7 sass scales scatterplot3d Seqinfo stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

lncRna: A Comprehensive Pipeline for lncRNA Identification and Functional Analysis

Rendered fromlncRna.Rmdusingknitr::rmarkdown

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

Help page	Topics
Aggregate Coding Potential Tool Results	aggregateCodPot
Annotate Genomic Interactions with Functional Enrichment Results	annotateInteractions
Evaluate Performance of Coding Potential Tools	bestTool
Evaluate Performance of Agreement Thresholds	bestToolAtleast
Evaluate Performance of Tool Combinations	bestToolCombination
Calculate and Filter Confusion Matrices for Tool Combinations	calculateCM
Split a Set of Sequence Names into Training and Test Sets	createTrainTestSets
Evaluate Performance of Tool Combinations	evaluateToolCombinations
Evaluate Agreement Thresholds Among Coding Potential Tools	evaluateToolsThresholds
Find Potential cis-Regulatory Interactions from FEELnc Output	findCisInteractions
Estimates trans-interactions between lncRNAs and target RNAs based on expression correlation. This function requires the 'Hmisc' and 'tidyr' packages.	findTransInteractions
Extract Gene or Transcript Biotypes from a GRanges Object	getBiotypes
Extract Transcript Statistics from a GTF object	getGtfStats
Create Clock Plots for Confusion Matrix Metrics	plotClockMetrics
Create Radar Plots for Confusion Matrix Metrics	plotRadarMetrics
Plot Functional Interactions as a Sankey Diagram	plotSankeyInteractions
Create Venn Diagram from Coding Potential Results	plotVennCodPot
Prepare Data Sets for Performance Evaluation	prepareEvaluationSets

Package: lncRna 1.1.0

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

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