NTW: Predict gene network using an Ordinary Differential Equation (ODE) based method

Package: NTW 1.63.0

Yuanhua Liu

NTW: Predict gene network using an Ordinary Differential Equation (ODE) based method

This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.

Authors:Wei Xiao, Yin Jin, Darong Lai, Xinyi Yang, Yuanhua Liu, Christine Nardini

NTW_1.63.0.tar.gz
NTW_1.63.0.zip(r-4.7)NTW_1.63.0.zip(r-4.6)NTW_1.63.0.zip(r-4.5)
NTW_1.63.0.tgz(r-4.6-any)NTW_1.63.0.tgz(r-4.5-any)
NTW_1.63.0.tar.gz(r-4.7-any)NTW_1.63.0.tar.gz(r-4.6-any)
NTW_1.63.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NTW/json (API)

# Install 'NTW' in R:

install.packages('NTW', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

sos.data - SOS pathway perturbation data

On BioConductor:NTW-1.63.0(bioc 3.24)NTW-1.62.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

preprocessing

3.78 score 2 scripts 3 mentions 10 exports 1 dependencies

Last updated from:5e5ce3152b. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	133
linux-devel-x86_64	WARNING	145
source / vignettes	OK	168
linux-release-x86_64	WARNING	128
macos-release-arm64	WARNING	67
macos-oldrel-arm64	WARNING	85
windows-devel	WARNING	77
windows-release	WARNING	62
windows-oldrel	WARNING	62
wasm-release	OK	117

Exports:A.estimation.Srow AP.estimation.Srow backward comb.matrix forward method.geo method.ml method.sse NTW P.preestimation

Dependencies:mvtnorm

NTW vignette

Introduction | Beginning NTW

Rendered fromNTW.Rnwusingutils::Sweave

Help page	Topics
Gene interaction network and perturbation targets predictions	NTW-package
Estimation of a single row in matrix A with the perturbation targets matrix P known	A.estimation.Srow
Estimation of a single row in gene interaction matrix A and perturbation targets matrix P	AP.estimation.Srow
Create all combinations of vectors	comb.matrix
Regression methods to estimate a single row in A with fixed perturbations	method.geo method.ml method.sse
Estimation of gene interaction matrix A and perturbation targets matrix P	NTW
Pre-estimation of the transcriptional pertubation targets matrix P	P.preestimation
Approaches to use a priori known gene association information for a single row estimation in matrix A	backward forward
SOS pathway perturbation data	sos.data

Help page

Topics

Gene interaction network and perturbation targets predictions

NTW-package

Estimation of a single row in matrix A with the perturbation targets matrix P known

A.estimation.Srow

Estimation of a single row in gene interaction matrix A and perturbation targets matrix P

AP.estimation.Srow

Create all combinations of vectors

comb.matrix

Regression methods to estimate a single row in A with fixed perturbations

method.geo method.ml method.sse