curatedAdipoChIP
This is the released version of curatedAdipoChIP; for the devel version, see curatedAdipoChIP.
A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
Bioconductor version: Release (3.23)
A curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy at students.kasralainy.edu.eg>
citation("curatedAdipoChIP")):
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("curatedAdipoChIP")
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("curatedAdipoChIP")| Using curatedAdipoChIP | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeqData, ExperimentData, ExperimentHub, GEO, SequencingData |
| Version | 1.28.0 |
| License | GPL-3 |
| Depends | R (>= 3.6), SummarizedExperiment, ExperimentHub |
| Imports | |
| System Requirements | |
| URL | https://github.com/MahShaaban/curatedAdipoChIP |
| Bug Reports | https://github.com/MahShaaban/curatedAdipoChIP/issues |
See More
| Suggests | knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi, S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr, tidyr, ggplot2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | curatedAdipoChIP_1.28.0.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/curatedAdipoChIP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/curatedAdipoChIP |
| Package Short Url | https://bioconductor.org/packages/curatedAdipoChIP/ |
| Package Downloads Report | Download Stats |