NanoporeRNASeq

DOI: 10.18129/B9.bioc.NanoporeRNASeq    

Nanopore RNA-Seq Example data

Bioconductor version: Release (3.12)

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 Developer [aut], Ying Chen Developer [cre], Yuk Kei Wan Developer [aut]

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

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script NanoporeRNASeq
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews ExperimentData, ExperimentHub, Genome, RNASeqData, SequencingData
Version 1.0.0
License GPL-3 + file LICENSE
Depends R (>= 4.0.0), ExperimentHub(>= 1.15.3)
Imports
LinkingTo
Suggests knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, GenomicAlignments, Rsamtools
SystemRequirements
Enhances parallel
URL https://github.com/GoekeLab/NanoporeRNASeq
Depends On Me
Imports Me
Suggests Me bambu
Links To Me
Build Report  

Package Archives

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

Source Package NanoporeRNASeq_1.0.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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