sechm
This is the released version of sechm; for the devel version, see sechm.
sechm: Complex Heatmaps from a SummarizedExperiment
Bioconductor version: Release (3.23)
sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.
Author: Pierre-Luc Germain [cre, aut]
Maintainer: Pierre-Luc Germain <pierre-luc.germain at hest.ethz.ch>
citation("sechm")):
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("sechm")
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("sechm")| sechm | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0), SummarizedExperiment, ComplexHeatmap |
| Imports | S4Vectors, seriation, circlize, methods, randomcoloR, stats, grid, grDevices, matrixStats |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/plger/sechm |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | SEtools |
| Imports Me | broadSeq |
| Suggests Me | OMA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sechm_1.20.0.tar.gz |
| Windows Binary (x86_64) | sechm_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | sechm_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | sechm_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sechm |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sechm |
| Bioc Package Browser | https://code.bioconductor.org/browse/sechm/ |
| Package Short Url | https://bioconductor.org/packages/sechm/ |
| Package Downloads Report | Download Stats |