blacksheepr
This is the released version of blacksheepr; for the devel version, see blacksheepr.
Outlier Analysis for pairwise differential comparison
Bioconductor version: Release (3.23)
Blacksheep is a tool designed for outlier analysis in the context of pairwise comparisons in an effort to find distinguishing characteristics from two groups. This tool was designed to be applied for biological applications such as phosphoproteomics or transcriptomics, but it can be used for any data that can be represented by a 2D table, and has two sub populations within the table to compare.
Author: MacIntosh Cornwell [aut], RugglesLab [cre]
Maintainer: RugglesLab <ruggleslab at gmail.com>
citation("blacksheepr")):
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("blacksheepr")
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("blacksheepr")| Outlier Analysis using blacksheepr - Phosphoprotein | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6) |
| Imports | grid, stats, grDevices, utils, circlize, viridis, RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ruggleslab/blacksheepr/issues |
See More
| Suggests | testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl |
| 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 | blacksheepr_1.26.0.tar.gz |
| Windows Binary (x86_64) | blacksheepr_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | blacksheepr_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | blacksheepr_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/blacksheepr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/blacksheepr |
| Bioc Package Browser | https://code.bioconductor.org/browse/blacksheepr/ |
| Package Short Url | https://bioconductor.org/packages/blacksheepr/ |
| Package Downloads Report | Download Stats |