nempi
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see nempi.
Inferring unobserved perturbations from gene expression data
Bioconductor version: 3.16
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")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.6.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 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 |
| 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_1.6.0.tar.gz |
| Windows Binary | nempi_1.6.0.zip |
| macOS Binary (x86_64) | nempi_1.6.0.tgz |
| macOS Binary (arm64) | nempi_1.6.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |