nempi
This is the development version of nempi; for the stable release version, see nempi.
Inferring unobserved perturbations from gene expression data
Bioconductor version: Development (3.24)
Takes as input an incomplete perturbation profile and differential gene expression in log odds and infers unobserved perturbations and augments observed ones. The inference is done by iteratively inferring a network from the perturbations and inferring perturbations from the network. The network inference is done by Nested Effects Models.
Author: Martin Pirkl [aut, cre]
Maintainer: Martin Pirkl <martinpirkl at yahoo.de>
citation("nempi")):
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("nempi")
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("nempi")| nempi | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, CRISPR, Classification, DNASeq, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneSignaling, Network, NetworkInference, NeuralNetwork, Pathways, PooledScreens, RNASeq, SingleCell, Software, SystemsBiology |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1), mnem |
| Imports | e1071, nnet, randomForest, naturalsort, graphics, stats, utils, matrixStats, epiNEM |
| System Requirements | |
| URL | https://github.com/cbg-ethz/nempi/ |
| Bug Reports | https://github.com/cbg-ethz/nempi/issues |
See More
| Suggests | knitr, BiocGenerics, rmarkdown, RUnit, 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 | nempi_1.21.0.tar.gz |
| Windows Binary (x86_64) | nempi_1.21.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | nempi_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | nempi_1.21.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/nempi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nempi |
| Bioc Package Browser | https://code.bioconductor.org/browse/nempi/ |
| Package Short Url | https://bioconductor.org/packages/nempi/ |
| Package Downloads Report | Download Stats |