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NanoporeRNASeq

Nanopore RNA-Seq Example data


Bioconductor version: Release (3.18)

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.

Author: Jonathan Goeke [aut], Ying Chen [cre], Yuk Kei Wan [aut]

Maintainer: Ying Chen <chen_ying at gis.a-star.edu.sg>

Citation (from within R, enter citation("NanoporeRNASeq")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NanoporeRNASeq")

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("NanoporeRNASeq")
NanoporeRNASeq HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ExperimentData, ExperimentHub, Genome, RNASeqData, SequencingData
Version 1.12.0
License GPL-3 + file LICENSE
Depends R (>= 4.0.0), ExperimentHub(>= 1.15.3)
Imports
System Requirements
URL https://github.com/GoekeLab/NanoporeRNASeq
See More
Suggests knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools
Linking To
Enhances parallel
Depends On Me
Imports Me
Suggests Me bambu
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package NanoporeRNASeq_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/NanoporeRNASeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NanoporeRNASeq
Package Short Url https://bioconductor.org/packages/NanoporeRNASeq/
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