Package 'QUBICdata'

Title: Data employed in the vignette of the QUBIC package
Description: The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10.
Authors: Yu Zhang [aut, cre], Qin Ma [aut]
Maintainer: Yu Zhang <[email protected]>
License: Unlimited | file LICENSE
Version: 1.40.0
Built: 2026-10-10 11:09:30 UTC
Source: https://github.com/bioc/QUBICdata

Help Index

E.coli

Description

Gene expression data matrix for experiments with E.coli from Many Microbe Microarrays Database (M3D).

Usage

data("ecoli")

Format

Large matrix with information about the expression levels of 4297 genes over 466 conditions.

Source

http://m3d.mssm.edu/

References

Faith, JJ et al. (2008) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 36 D866-70

Examples

data(ecoli)
## maybe str(ecoli) ; plot(ecoli) ...

E.coli Weight

Description

Protein network information (scored links between proteins) for Escherichia coli K12 MG1655. It originates from STRING v10 and serves as example weight input for the query-based biclustering function in QUBIC.

Usage

data("ecoli.weight")

Format

Large dgcMatrix with information about the weight between proteins.

Source

http://string-db.org/download/protein.links.v10/511145.protein.links.v10.txt.gz

References

Szklarczyk, D et al. (2014) STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43 D447–52

Examples

data(ecoli.weight)
## maybe str(ecoli.weight) ; plot(ecoli.weight) ...