cooccurNet: Co-Occurrence Network

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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 SNP.

Author
Yuanqiang Zou <jerrytsou2001@gmail.com>, Yousong Peng <pys2013@hnu.edu.cn> and Taijiao Jiang <taijiao@moon.ibp.ac.cn>
Date of publication
2016-09-20 09:10:41
Maintainer
Yuanqiang Zou <jerrytsou2001@gmail.com>
License
GPL-3
Version
0.1.3

View on CRAN

Man pages

cooccurNet
cooccurNet: Co-Occurrence network computation for R
coocnet
coocnet
gencooccur
gencooccur
getexample
getexample
getexample_forRCOS
getexample_forRCOS
pprocess
pprocess
readseq
readseq
siteco
siteco
toigraph
toigraph

Files in this package

cooccurNet
cooccurNet/inst
cooccurNet/inst/extdata
cooccurNet/inst/extdata/protein
cooccurNet/inst/extdata/DNA
cooccurNet/inst/extdata/RCOS
cooccurNet/inst/extdata/RCOS/HA1protein_humanH3N2
cooccurNet/inst/extdata/SNP
cooccurNet/NAMESPACE
cooccurNet/R
cooccurNet/R/gennetwork.R
cooccurNet/R/datapreprocess.R
cooccurNet/R/cooccurrence.R
cooccurNet/R/pubfuncs.R
cooccurNet/R/readfasta.R
cooccurNet/R/networkpvalue.R
cooccurNet/MD5
cooccurNet/DESCRIPTION
cooccurNet/man
cooccurNet/man/getexample.Rd
cooccurNet/man/pprocess.Rd
cooccurNet/man/getexample_forRCOS.Rd
cooccurNet/man/readseq.Rd
cooccurNet/man/gencooccur.Rd
cooccurNet/man/cooccurNet.Rd
cooccurNet/man/coocnet.Rd
cooccurNet/man/siteco.Rd
cooccurNet/man/toigraph.Rd