Package 'HumanRetinaLRSData'

Title: Long-read RNA-seq gene count data from human retinal organoids
Description: 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.
Authors: Sowmya Parthiban [aut, cre]
Maintainer: Sowmya Parthiban <[email protected]>
License: MIT + file LICENSE
Version: 1.1.0
Built: 2026-10-10 10:47:05 UTC
Source: https://github.com/bioc/HumanRetinaLRSData

Help Index

Allele-specific expression (ASE) gene counts

Description

Allele-specific expression (ASE) gene counts

Usage

ASEGeneCounts()

Value

A numeric matrix

Examples

ase_counts <- ASEGeneCounts()
head(ase_counts)

Clear OSF cache

Description

Clear OSF cache

Usage

clear_osf_cache(
  bfc = BiocFileCache::BiocFileCache(tools::R_user_dir("HumanRetinaLRSData", which =
    "cache"), ask = FALSE)
)

Arguments

bfc

BiocFileCache object

Value

NULL (invisibly). Called for side effect of clearing cache.

Examples

clear_osf_cache()

Gene-level counts for flow through (FT) and retinal ganglion cell (RGC) samples

Description

Gene-level counts for flow through (FT) and retinal ganglion cell (RGC) samples

Usage

FTRGCGeneLevelData()

Value

A SummarizedExperiment object

Examples

ftrgc_data <- FTRGCGeneLevelData()
ftrgc_data

Isoform-level counts for flow through (FT) and retinal ganglion cell (RGC) samples

Description

Isoform-level counts for flow through (FT) and retinal ganglion cell (RGC) samples

Usage

FTRGCIsoformLevelData()

Value

A SummarizedExperiment object

Examples

ftrgc_iso_data <- FTRGCIsoformLevelData()
ftrgc_iso_data

List available files on OSF

Description

List available files on OSF

Usage

list_osf_files()

Value

Character vector of file names

Examples

list_osf_files()

Load a dataset from OSF with BiocFileCache

Description

Validates osf_file_name against the bundled ‘inst/extdata/metadata.csv’ (no internet connection required for validation). On first use the data files are downloaded from OSF and cached via BiocFileCache; subsequent calls load from the local cache.

Usage

load_object(
  osf_file_name,
  bfc = BiocFileCache::BiocFileCache(tools::R_user_dir("HumanRetinaLRSData", which =
    "cache"), ask = FALSE)
)

Arguments

osf_file_name

Character scalar. Dataset base name; see list_osf_files.
bfc

A BiocFileCache object. Defaults to a per-user package cache.

Value

A SummarizedExperiment or a matrix, depending on the dataset.

Examples

## Not run: 
se <- load_object("ROGeneLevelData")
se

## End(Not run)

Gene-level counts for retinal organoid (RO) samples

Description

Gene-level counts for retinal organoid (RO) samples

Usage

ROGeneLevelData()

Value

A SummarizedExperiment object

Examples

ro_data <- ROGeneLevelData()
ro_data

Isoform-level counts for retinal organoid (RO) samples

Description

Isoform-level counts for retinal organoid (RO) samples

Usage

ROIsoformLevelData()

Value

A SummarizedExperiment object

Examples

ro_iso_data <- ROIsoformLevelData()
ro_iso_data