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.

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

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Files

cooccurNet
cooccurNet/inst
cooccurNet/inst/extdata
cooccurNet/inst/extdata/changeLog
cooccurNet/inst/extdata/changeLog/changeLog
cooccurNet/inst/extdata/protein
cooccurNet/inst/extdata/DNA
cooccurNet/inst/extdata/RNA
cooccurNet/inst/extdata/RCOS
cooccurNet/inst/extdata/RCOS/HA1protein_humanH3N2
cooccurNet/inst/extdata/SNP
cooccurNet/inst/doc
cooccurNet/inst/doc/Extending-cooccurNet.Rmd
cooccurNet/inst/doc/Extending-cooccurNet.html
cooccurNet/inst/doc/Extending-cooccurNet.R
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/vignettes
cooccurNet/vignettes/Extending-cooccurNet.Rmd
cooccurNet/MD5
cooccurNet/build
cooccurNet/build/vignette.rds
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/changeLog.Rd cooccurNet/man/siteco.Rd cooccurNet/man/toigraph.Rd

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

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