nempi
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see nempi.
Inferring unobserved perturbations from gene expression data
Bioconductor version: 3.19
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 "4.4") 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 | 1.12.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_1.12.0.tar.gz |
Windows Binary (x86_64) | nempi_1.12.0.zip |
macOS Binary (x86_64) | nempi_1.12.0.tgz |
macOS Binary (arm64) | nempi_1.12.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/nempi |
Source Repository (Developer Access) | git clone [email protected]:packages/nempi |
Bioc Package Browser | https://code.bioconductor.org/browse/nempi/ |
Package Short Url | https://bioconductor.org/packages/nempi/ |
Package Downloads Report | Download Stats |