Package: KINNET 0.4.0.9002

Ali Sajid Imami

KINNET: Kinase INteraction NETwork Generation

This package provides the functionality to process PamGene's PamChip Data Output and generate kinase interaction networks from that. This project uses a bayesian algorithm to generate bayesian networks for defining dependence relationships between peptide sequences in the PamChip data. It then uses a novel kinase assignment method to assign upstream kinases to each peptide which is then output as a graph.

Authors:Ali Sajid Imami [aut, cre], Khaled Alganem [aut], Justin Fortune Creeden [aut], Alex Joyce [aut]

KINNET_0.4.0.9002.tar.gz
KINNET_0.4.0.9002.zip(r-4.5)KINNET_0.4.0.9002.zip(r-4.4)
KINNET_0.4.0.9002.tgz(r-4.4-any)
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KINNET_0.4.0.9002.tgz(r-4.4-emscripten)
KINNET.pdf |KINNET.html✨
KINNET/json (API)

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

Peer review:

Bug tracker:https://github.com/cogdisreslab/kinnet/issues

On CRAN:

2.00 score 2 stars 3 scripts 21 exports 41 dependencies

Last updated 3 years agofrom:8c901f74fe. Checks:OK: 1 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winWARNINGOct 27 2024
R-4.5-linuxWARNINGOct 27 2024
R-4.4-winWARNINGOct 27 2024
R-4.4-macWARNINGOct 27 2024

Exports:assign_kinasesassign_kinases_guidedclassescompare_kinased_graphsequalize_kinase_graphsexp_datafilter_peptidesfit_standardizedkinnet_hammingkinnet_normalized_hammingkinnet_normalized_shdkinnet_shdmake_modelPamchipData_PTKPamchipData_STKpeptidespheno_datarender_kinased_graphrender_reduced_kinased_graphsubset_dataupdate_probability_matrix

Dependencies:bayestestRBiocGenericsbitbit64bnlearnclicliprcpp11crayondatawizarddplyreffectsizefansigenericsgluegraphhmsinsightlifecyclemagrittrparametersperformancepillarpkgconfigprettyunitsprogresspurrrR6readrRgraphvizrlangstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Readme and manuals

Help Manual

Help pageTopics
Assign kinases, given a network and a chip typeassign_kinases
Assign kinases, given a network and a chip type and additional essential kinasesassign_kinases_guided
Generate Candidate Kinases Based On Linkscandidate_kinases
Compare two kinased graphhscompare_kinased_graphs
Equalize the nodesets of two kinased graphsequalize_kinase_graphs
Return a list of significant peptidesfilter_peptides
Do a standardized fit of expression data from a single peptide's activityfit_standardized
Generate Intersections between kinasesget_intersections
Calculate the Hamming Distance between two kinased graphskinnet_hamming
Calculate Normalized Hamming Distancekinnet_normalized_hamming
Calculate Normalized Structural Hamming Distancekinnet_normalized_shd
Calculate the Structural Hamming Distance between two kinased graphskinnet_shd
Generate a bayes net modelmake_model
Process a file into a usable structurePamchipData_PTK
Process a file into a usable structurePamchipData_STK
The Pamchip Data SuperclassPamchipData-class
A representation of the PamChip PTK DataPamchipData-PTK-class
A representation of the PamChip STK DataPamchipData-STK-class
PTK Peptide to Kinase Probability Matrix for Gene Identifiersptk_probability_matrix_gene
PTK Peptide to Kinase Probability Matrix for Kinase Identifiersptk_probability_matrix_kinase
Generate a kianse graphrender_kinased_graph
Generate a reduced kianse graphrender_reduced_kinased_graph
Add a node safely to a bn objectsafely_add_node
STK Data Accessor Functionsclasses classes,PamchipData-STK-method exp_data exp_data,PamchipData-STK-method peptides peptides,PamchipData-STK-method pheno_data pheno_data,PamchipData-STK-method stk_accessors
STK Peptide to Kinase Probability Matrix for Gene Identifiersstk_probability_matrix_gene
STK Peptide to Kinase Probability Matrix for Kinase Identifiersstk_probability_matrix_kinase
Subset The Kinome Datasubset_data
Calculated Updated Probabilities of each peptide/kinase pairupdate_probability_matrix