HumanRetinaLRSData
Long-read RNA-seq gene count data from human retinal organoids
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Dataset package containing gene and isoform count matrices, and sample metadata for long-read direct cDNA sequencing of human retinal organoids, 2D retinal ganglion cell (RGC) cultures, and flowthrough fractions from H9 and EP1 iPSC cell lines. Data were generated using Oxford Nanopore Technology (ONT) direct cDNA sequencing and mapped to the GRCh38 reference genome (GENCODE v46 annotation). The package provides accessor functions returning SummarizedExperiment objects for gene-level counts, isoform-level counts, and a matrix of allele-specific expression (ASE) gene counts. Data files are stored in flat CSV format in an Open Science Framework (OSF) repository and cached locally via BiocFileCache.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HumanRetinaLRSData")Details
| Maintainer | Sowmya Parthiban <sparthi1@jhu.edu> |
| Author | Sowmya Parthiban [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/sparthib/HumanRetinaLrsData |
| Bug Reports | https://github.com/sparthib/HumanRetinaLrsData/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellCulture, ExperimentData, ExpressionData, Homo_sapiens_Data, RNASeqData |
| Package Short Url | https://bioconductor.org/packages/HumanRetinaLRSData/ |
Citation
From within R, enter citation("HumanRetinaLRSData"):
Sowmya Parthiban. HumanRetinaLRSData: Long-read RNA-seq gene count data from human retinal organoids. doi:10.18129/B9.bioc.HumanRetinaLRSData, R package version 1.0.0, https://bioconductor.org/packages/HumanRetinaLRSData.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | HumanRetinaLRSData_1.0.0.tar.gz |