Corbi: Collection of Rudimentary Bioinformatics Tools

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Provides a bundle of basic and fundamental bioinformatics tools, such as network querying and alignment, subnetwork extraction and search, network biomarker identification.

Author
Ling-Yun Wu [aut, cre], Qiang Huang [aut], Duanchen Sun [aut]
Date of publication
2016-09-20 18:46:37
Maintainer
Ling-Yun Wu <wulingyun@gmail.com>
License
GPL (>= 2)
Version
0.4-1
URLs

View on CRAN

Man pages

best_subnets
The best subnetworks
column
Extract a column from a matrix
Corbi-package
Corbi - Collection of Rudimentary Bioinformatics Tools
extend_subnets
Extend subnetworks from smaller subnetworks
get_shortest_distances
Calculate shortest distances of unweighted network
get_subnets
All subnetworks of limited size
kappa_score
Cohen's kappa score
markrank
MarkRank
net_align
Network alignment method based on conditional random fields
net_query
Network querying method based on conditional random fields
nnzero
The number of non-zero values of a submatrix
read_net
Read network information from text file
rmultihyper
The Multivariate Hypergeometric Distribution
submatrix
Extract a submatrix from a matrix
write_net
Write network information to text file

Files in this package

Corbi
Corbi/tests
Corbi/tests/net_align
Corbi/tests/net_align/answer1_uni.txt
Corbi/tests/net_align/net1.txt
Corbi/tests/net_align/answer1.txt
Corbi/tests/net_align/sim.txt
Corbi/tests/net_align/net2.txt
Corbi/tests/net_align/net3.txt
Corbi/tests/test_net_query.R
Corbi/tests/test_markrank.R
Corbi/tests/markrank
Corbi/tests/markrank/de_list.RData
Corbi/tests/markrank/subnetwork.txt
Corbi/tests/markrank/answer.RData
Corbi/tests/markrank/dataset.RData
Corbi/tests/markrank/search_net.R
Corbi/tests/test_net_align.R
Corbi/tests/net_query
Corbi/tests/net_query/target.txt
Corbi/tests/net_query/answer1.txt
Corbi/tests/net_query/query1.txt
Corbi/tests/net_query/answer2.txt
Corbi/tests/net_query/sim.txt
Corbi/tests/net_query/query2.txt
Corbi/src
Corbi/src/ProAlign.cpp
Corbi/src/misc.cpp
Corbi/src/Subnets.cpp
Corbi/src/misc.h
Corbi/src/Corbi.cpp
Corbi/src/Corbi.h
Corbi/src/NetQuery.cpp
Corbi/src/multihyper.cpp
Corbi/NAMESPACE
Corbi/R
Corbi/R/utils.R
Corbi/R/net_functions.R
Corbi/R/net_align.R
Corbi/R/net_query_batch.R
Corbi/R/multihyper.R
Corbi/R/net_query.R
Corbi/R/subnets.R
Corbi/R/markrank.R
Corbi/R/pro_align.R
Corbi/R/Corbi-package.R
Corbi/README.md
Corbi/MD5
Corbi/DESCRIPTION
Corbi/man
Corbi/man/write_net.Rd
Corbi/man/Corbi-package.Rd
Corbi/man/nnzero.Rd
Corbi/man/submatrix.Rd
Corbi/man/kappa_score.Rd
Corbi/man/get_shortest_distances.Rd
Corbi/man/rmultihyper.Rd
Corbi/man/column.Rd
Corbi/man/net_align.Rd
Corbi/man/extend_subnets.Rd
Corbi/man/best_subnets.Rd
Corbi/man/markrank.Rd
Corbi/man/get_subnets.Rd
Corbi/man/net_query.Rd
Corbi/man/read_net.Rd