Required packages | Overview | Load data | Visualise gene-level expression | Visualise isoform-level expression | Interpretation | Session information
Package: HumanRetinaLRSData 1.1.0
Sowmya Parthiban
HumanRetinaLRSData: Long-read RNA-seq gene count data from human retinal organoids
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:
HumanRetinaLRSData_1.1.0.tar.gz
HumanRetinaLRSData_1.1.0.tar.gz(r-4.7-any)HumanRetinaLRSData_1.1.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
HumanRetinaLRSData/json (API)
| # Install 'HumanRetinaLRSData' in R: |
| install.packages('HumanRetinaLRSData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sparthib/humanretinalrsdata/issues
On BioConductor:HumanRetinaLRSData-1.1.0(data/experiment 3.24)HumanRetinaLRSData-1.0.0(data/experiment 3.23)
experimentdatarnaseqdataexpressiondatahomo_sapiens_datacellculturedatapkg
Last updated from:85415f64fb. Checks:1 NOTE, 3 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 181 | ||
| linux-devel | OK | 376 | ||
| source / vignettes | OK | 458 | ||
| linux-release | OK | 341 |
Exports:ASEGeneCountsclear_osf_cacheFTRGCGeneLevelDataFTRGCIsoformLevelDatalist_osf_filesload_objectROGeneLevelDataROIsoformLevelData
Dependencies:abindaskpassBiobaseBiocFileCacheBiocGenericsbitbit64blobcachemclicpp11crulcurlDBIdbplyrDelayedArraydplyrfastmapfilelockfsgenericsGenomicRangesgluehttpcodehttrhttr2IRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslosfrpillarpkgconfigpurrrR6RcpprlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttriebeardurltoolsutf8vctrswithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Allele-specific expression (ASE) gene counts | ASEGeneCounts |
| Clear OSF cache | clear_osf_cache |
| Gene-level counts for flow through (FT) and retinal ganglion cell (RGC) samples | FTRGCGeneLevelData |
| Isoform-level counts for flow through (FT) and retinal ganglion cell (RGC) samples | FTRGCIsoformLevelData |
| List available files on OSF | list_osf_files |
| Load a dataset from OSF with BiocFileCache | load_object |
| Gene-level counts for retinal organoid (RO) samples | ROGeneLevelData |
| Isoform-level counts for retinal organoid (RO) samples | ROIsoformLevelData |