NanoporeRNASeq

This is the released version of NanoporeRNASeq; for the devel version, see NanoporeRNASeq.

Nanopore RNA-Seq Example data

Bioconductor version: Release (3.20)

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, Genome, RNASeqData, SequencingData
Version	1.16.0
License	GPL-3 + file LICENSE
Depends	R (>= 4.0.0), ExperimentHub(>= 1.15.3)
Imports
System Requirements
URL	https://github.com/GoekeLab/NanoporeRNASeq

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_1.16.0.tar.gz
Windows Binary (x86_64)
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/
Package Downloads Report	Download Stats