Package: OrnTx 0.99.2

Lashika Meena

OrnTx: Expression Atlas for Ornamental Plant Transcriptomics

The first R/Bioconductor package for ornamental plant transcriptomics. Provides a complete RNA-seq pipeline (download, QC, alignment, import), a curated Rosa chinensis expression atlas, a 64-gene floriculture trait database anchored to Arabidopsis orthologs, multi-tool import support (STAR, featureCounts, HTSeq, Salmon), auto-detection of three Rosa chinensis gene ID formats, and cross-species validation on Tagetes erecta.

Authors:Lashika Meena [aut, cre]

OrnTx_0.99.2.tar.gz
OrnTx_0.99.2.zip(r-4.7-any)OrnTx_0.99.2.zip(r-4.6-any)OrnTx_0.99.2.zip(r-4.5-any)
OrnTx_0.99.2.tgz(r-4.6-any)OrnTx_0.99.2.tgz(r-4.5-any)
OrnTx_0.99.2.tar.gz(r-4.7-any)OrnTx_0.99.2.tar.gz(r-4.6-any)
OrnTx_0.99.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
OrnTx/json (API)

# Install 'OrnTx' in R:

install.packages('OrnTx', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lashikakarnal/orntx/issues

Datasets:

floriculture_traits - Floriculture Trait Gene Database
marigold_carotenoid_genes - Marigold Carotenoid Gene Mapping
rosa_annotation - Rosa chinensis Gene Annotation Database
rosa_example - Rosa chinensis Example Expression Dataset
rose_ncbi_annotation - Rosa chinensis NCBI Functional Annotation

On CRAN:

rnaseq geneexpression differentialexpression transcriptomics visualization dataimport annotation alignment

3.04 score 4 scripts 25 exports 45 dependencies

Last updated from:34ba0effa9. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	152
linux-devel	WARNING	183
source / vignettes	OK	191
linux-release	WARNING	155
macos-release	WARNING	122
macos-oldrel	WARNING	139
windows-devel	WARNING	126
windows-release	WARNING	121
windows-oldrel	WARNING	122
wasm-release	OK	127

Exports:alignReads annotateDEResults annotateGenes annotateWithNCBI annotateWithTraits buildAtlas buildGenomeIndex buildRosaAtlas checkTools downloadSRA findOrthologs getFlowerGenes getRosaAnnotation importCountMatrix importCustomAtlas importRosaCounts normalizeCounts ornTheme plotAtlas plotPCA plotVolcano runDE runFullPipeline runQC standardizeStage

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray dplyr farver generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pillar pkgconfig purrr R6 RColorBrewer rlang S4Arrays S4Vectors S7 scales Seqinfo SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

OrnTx: Expression Atlas for Ornamental Plants

Rendered fromOrnTx_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-09-25
Started: 2026-09-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Align RNA-seq reads using STAR	alignReads
Annotate DE results	annotateDEResults
Annotate gene IDs with Rosa chinensis locus information	annotateGenes
Annotate gene IDs using NCBI functional annotation	annotateWithNCBI
Annotate DE results with trait information	annotateWithTraits
Build an expression atlas from count data	buildAtlas
Build STAR genome index	buildGenomeIndex
Build Rosa chinensis Expression Atlas	buildRosaAtlas
Check which RNA-seq tools are available	checkTools
Download RNA-seq data from NCBI SRA	downloadSRA
Find orthologs in floriculture trait database	findOrthologs
Floriculture Trait Gene Database	floriculture_traits
Get curated floriculture trait gene sets	getFlowerGenes
Get Rosa chinensis annotation database	getRosaAnnotation
Import count data from any RNA-seq tool	importCountMatrix
Import RNA-seq data from any plant species into OrnTx	importCustomAtlas
Import STAR count files into OrnTx	importRosaCounts
Marigold Carotenoid Gene Mapping	marigold_carotenoid_genes
Normalize count data	normalizeCounts
OrnTx ggplot2 theme	ornTheme
Plot expression atlas heatmap	plotAtlas
PCA plot of expression data	plotPCA
Volcano plot of DE results	plotVolcano
Rosa chinensis Gene Annotation Database	rosa_annotation
Rosa chinensis Example Expression Dataset	rosa_example
Rosa chinensis NCBI Functional Annotation	rose_ncbi_annotation
Differential Expression Analysis	runDE
Run complete RNA-seq pipeline from FASTQ to SummarizedExperiment	runFullPipeline
Quality control of FASTQ files using fastp	runQC
Standardize developmental stage vocabulary	standardizeStage