macrophage
This is the released version of macrophage; for the devel version, see macrophage.
Human macrophage immune response
Bioconductor version: Release (3.23)
This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette.
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("macrophage")):
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("macrophage")
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("macrophage")| Salmon quantifications for human macrophage immune response experiment | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, RNASeqData, SequencingData |
| Version | 1.28.0 |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, markdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | DeeDeeExperiment, fishpond, GeDi, GeneTonic, mosdef, quantiseqr, tximeta, fluentGenomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | macrophage_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/macrophage |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/macrophage |
| Package Short Url | https://bioconductor.org/packages/macrophage/ |
| Package Downloads Report | Download Stats |