Package: Corbi 0.6-2

Corbi: Collection of Rudimentary Bioinformatics Tools

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

Authors:Ling-Yun Wu [aut, cre], Qiang Huang [aut], Duanchen Sun [aut]

Corbi_0.6-2.tar.gz
Corbi_0.6-2.zip(r-4.5)Corbi_0.6-2.zip(r-4.4)Corbi_0.6-2.zip(r-4.3)
Corbi_0.6-2.tgz(r-4.4-x86_64)Corbi_0.6-2.tgz(r-4.4-arm64)Corbi_0.6-2.tgz(r-4.3-x86_64)Corbi_0.6-2.tgz(r-4.3-arm64)
Corbi_0.6-2.tar.gz(r-4.5-noble)Corbi_0.6-2.tar.gz(r-4.4-noble)
Corbi_0.6-2.tgz(r-4.4-emscripten)Corbi_0.6-2.tgz(r-4.3-emscripten)
Corbi.pdf |Corbi.html✨
Corbi/json (API)

# Install 'Corbi' in R:
install.packages('Corbi', repos = c('https://wulingyun.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/wulingyun/corbi/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

5.95 score 6 stars 30 scripts 208 downloads 5 mentions 33 exports 13 dependencies

Last updated 3 years agofrom:335f1febb9. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-win-x86_64NOTEOct 24 2024
R-4.5-linux-x86_64NOTEOct 24 2024
R-4.4-win-x86_64OKNov 23 2024
R-4.4-mac-x86_64OKNov 23 2024
R-4.4-mac-aarch64OKNov 23 2024
R-4.3-win-x86_64OKNov 23 2024
R-4.3-mac-x86_64OKNov 23 2024
R-4.3-mac-aarch64OKNov 23 2024

Exports:best_subnetscolumnextend_subnetsget_adjusted_deg_diffget_diff_ratio_netget_ratio_distributionget_ratio_distribution2get_ratio_varianceget_shortest_distancesget_subnetskappa_scoremake_DEG_datamake_DEG_data2make_DEG_patternmarkranknet_alignnet_querynet_query_batchnetDEGnetDEG_pvaluennzerop_combinepmultihyperpmultinomread_netrmultihypersimulate_dropoutsimulate_dropout2simulate_sample_groupssubmatrixURG_getFactorURG_normalizewrite_net

Dependencies:clicpp11CRFglueigraphlatticelifecyclemagrittrMASSMatrixpkgconfigrlangvctrs

MarkRank Tutorial

Duanchen Sun and Ling-Yun Wu

Rendered fromMarkRank.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2017-04-29
Started: 2017-04-29

Readme and manuals

Help Manual

Help pageTopics
Corbi - Collection of Rudimentary Bioinformatics ToolsCorbi-package Corbi
The best subnetworksbest_subnets
Extract a column from a matrixcolumn
Extend subnetworks from smaller subnetworksextend_subnets
Calculate adjusted degree differences for given networkget_adjusted_deg_diff
Construct differential expression ratio networkget_diff_ratio_net
Calculate expression ratio distributionget_ratio_distribution
Calculate expression ratio distributionget_ratio_distribution2
Calculate expression ratio variancesget_ratio_variance
Calculate shortest distances of unweighted networkget_shortest_distances
All subnetworks of limited sizeget_subnets
Cohen's kappa scorekappa_score
Simulate differentially expressed gene data (Gaussian)make_DEG_data
Simulate differentially expressed gene data (Negative binomial)make_DEG_data2
Simulate differentially expressed gene patternmake_DEG_pattern
MarkRankmarkrank
Network alignment method based on conditional random fieldsnet_align
Network querying method based on conditional random fieldsnet_query net_query_batch
netDEG: Differentially expressed gene identification methodnetDEG
Calculate netDEG p-valuesnetDEG_pvalue
The number of non-zero values of a submatrixnnzero
Calculate combined p-valuep_combine
The Multivariate Hypergeometric Distributionpmultihyper
The Multinomial Distributionpmultinom
Read network information from text fileread_net
The Multivariate Hypergeometric Distributionrmultihyper
Simulate dropout expression datasimulate_dropout
Simulate dropout expression datasimulate_dropout2
Simulate sample groups from given samples with labelssimulate_sample_groups
Extract a submatrix from a matrixsubmatrix
Calculate normalization factors for URG methodURG_getFactor
Normalize using given factorsURG_normalize
Write network information to text filewrite_net