| Title: | Nanopore RNA-Seq Example data |
|---|---|
| Description: | The NanoporeRNASeq package contains long read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7) that were generated by the SG-NEx project. Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. |
| Authors: | Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut] |
| Maintainer: | Ying Chen <[email protected]> |
| License: | GPL-3 + file LICENSE |
| Version: | 1.23.1 |
| Built: | 2026-10-10 10:44:37 UTC |
| Source: | https://github.com/bioc/NanoporeRNASeq |
Annotation GRangesList prepared from bambu for Granges of human genome (Grch38) chromosome 22 (1:25409234)
data("HsChr22BambuAnnotation")data("HsChr22BambuAnnotation")
SummarizedExperiment
The NanoporeRNASeq package contains long-read RNA-Seq data generated using Oxford Nanopore Sequencing. The data consists of 6 samples from two human cell lines (K562 and MCF7). Each of these cell lines has three replicates, with 1 direct RNA sequencing data and 2 cDNA sequencing data. Reads are aligned to chromosome 22 (Grch38) and stored as bam files. The original data is from the SG-NEx project. Please see the package vignette for examples and use cases.
Data objects include:
SGNexSamples - sample information of the bam files
HsChr22BambuAnnotation - annotation GRangesList
For detailed information on usage, see the package vignette, by typing vignette("NanoporeRNASeq"), or the workflow linked to on the first page of the vignette.
Ying Chen, Yuk Kei Wan, Jonathan Göke
Sample information description for K562 and MCF7 samples from SG-Nex
data("SGNexSamples")data("SGNexSamples")
DataFrame
SGNexSamples is a DataFrame containing the following information:
sample_id - sample names of the bam files
Platform - sequencing platform
cellLine - cell line used
protocol - sequencing protocols
cancer_type- cancer type of the cell line