cooccurNet: Co-Occurrence Network

Read and preprocess fasta format data, and construct the co-occurrence network for downstream analyses. This R package is to construct the co-occurrence network with the algorithm developed by Du (2008) <DOI:10.1101/gr.6969007>. It could be used to transform the data with high-dimension, such as DNA or protein sequence, into co-occurrence networks. Co-occurrence network could not only capture the co-variation pattern between variables, such as the positions in DNA or protein sequences, but also reflect the relationship between samples. Although it is originally used in DNA and protein sequences, it could be also used to other kinds of data, such as RNA, SNP, etc.

Install the latest version of this package by entering the following in R:
install.packages("cooccurNet")
AuthorYuanqiang Zou <jerrytsou2001@gmail.com>, Yousong Peng <pys2013@hnu.edu.cn> and Taijiao Jiang <taijiao@moon.ibp.ac.cn>
Date of publication2017-01-27 10:38:24
MaintainerYuanqiang Zou <jerrytsou2001@gmail.com>
LicenseGPL-3
Version0.1.6

View on CRAN

Files

inst
inst/extdata
inst/extdata/changeLog
inst/extdata/changeLog/changeLog
inst/extdata/protein
inst/extdata/DNA
inst/extdata/RNA
inst/extdata/RCOS
inst/extdata/RCOS/HA1protein_humanH3N2
inst/extdata/SNP
inst/doc
inst/doc/Extending-cooccurNet.Rmd
inst/doc/Extending-cooccurNet.html
inst/doc/Extending-cooccurNet.R
NAMESPACE
R
R/gennetwork.R R/datapreprocess.R R/cooccurrence.R R/pubfuncs.R R/readfasta.R R/networkpvalue.R
vignettes
vignettes/Extending-cooccurNet.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getexample.Rd man/pprocess.Rd man/getexample_forRCOS.Rd man/readseq.Rd man/gencooccur.Rd man/cooccurNet.Rd man/coocnet.Rd man/changeLog.Rd man/siteco.Rd man/toigraph.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.