HERON
This is the released version of HERON; for the devel version, see HERON.
Hierarchical Epitope pROtein biNding
Bioconductor version: Release (3.23)
HERON is a software package for analyzing peptide binding array data. In addition to identifying significant binding probes, HERON also provides functions for finding epitopes (string of consecutive peptides within a protein). HERON also calculates significance on the probe, epitope, and protein level by employing meta p-value methods. HERON is designed for obtaining calls on the sample level and calculates fractions of hits for different conditions.
Author: Sean McIlwain [aut, cre]
, Irene Ong [aut]
Maintainer: Sean McIlwain <sean.mcilwain at wisc.edu>
citation("HERON")):
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("HERON")
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("HERON")| Analyzing High Density Peptide Array Data using HERON | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Microarray, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.4.0), SummarizedExperiment(>= 1.1.6), GenomicRanges, IRanges, S4Vectors |
| Imports | matrixStats, stats, data.table, harmonicmeanp, metap, cluster, spdep, Matrix, limma, methods |
| System Requirements | |
| URL | https://github.com/Ong-Research/HERON |
| Bug Reports | https://github.com/Ong-Research/HERON/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| 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 | HERON_1.10.0.tar.gz |
| Windows Binary (x86_64) | HERON_1.10.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | HERON_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | HERON_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HERON |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HERON |
| Bioc Package Browser | https://code.bioconductor.org/browse/HERON/ |
| Package Short Url | https://bioconductor.org/packages/HERON/ |
| Package Downloads Report | Download Stats |