NanoporeRNASeq
This is the released version of NanoporeRNASeq; for the devel version, see NanoporeRNASeq.
Nanopore RNA-Seq Example data
Bioconductor version: Release (3.23)
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("NanoporeRNASeq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Genome, RNASeqData, SequencingData |
| Version | 1.22.0 |
| 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |