moanin
This is the development version of moanin; for the stable release version, see moanin.
An R Package for Time Course RNASeq Data Analysis
Bioconductor version: Development (3.24)
Simple and efficient workflow for time-course gene expression data, built on publictly available open-source projects hosted on CRAN and bioconductor. moanin provides helper functions for all the steps required for analysing time-course data using functional data analysis: (1) functional modeling of the timecourse data; (2) differential expression analysis; (3) clustering; (4) downstream analysis.
Author: Elizabeth Purdom [aut]
, Nelle Varoquaux [aut, cre]
Maintainer: Nelle Varoquaux <nelle.varoquaux at gmail.com>
citation("moanin")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("moanin")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Clustering, DifferentialExpression, GeneExpression, Microarray, RNASeq, Software, TimeCourse |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | BSD 3-clause License + file LICENSE |
| Depends | R (>= 4.0), SummarizedExperiment, topGO, stats |
| Imports | S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats |
| System Requirements | |
| URL |
See More
| Suggests | testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/moanin |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/moanin |
| Package Short Url | https://bioconductor.org/packages/moanin/ |
| Package Downloads Report | Download Stats |