HumanRetinaLRSData
This is the development version of HumanRetinaLRSData; to use it, please install the devel version of Bioconductor.
Long-read RNA-seq gene count data from human retinal organoids
Bioconductor version: Development (3.23)
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.
Author: Sowmya Parthiban [aut, cre]
Maintainer: Sowmya Parthiban <sparthi1 at jhu.edu>
citation("HumanRetinaLRSData")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("HumanRetinaLRSData")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HumanRetinaLRSData")| Retinal Organoids counts data: Gene and Isoform Level Exploration | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellCulture, ExperimentData, ExpressionData, Homo_sapiens_Data, RNASeqData |
| Version | 0.99.5 |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0), SummarizedExperiment |
| Imports | osfr, BiocFileCache |
| System Requirements | |
| URL | https://github.com/sparthib/HumanRetinaLrsData |
| Bug Reports | https://github.com/sparthib/HumanRetinaLrsData/issues |
See More
| Suggests | testthat, knitr, rmarkdown, ggplot2, ggrepel |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HumanRetinaLRSData_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/HumanRetinaLRSData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HumanRetinaLRSData |
| Package Short Url | https://bioconductor.org/packages/HumanRetinaLRSData/ |
| Package Downloads Report | Download Stats |