Package: crosstalkr 1.0.5

Davis Weaver

crosstalkr: Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks

Provides a general toolkit for drug target identification. We include functionality to reduce large graphs to subgraphs and prioritize nodes. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Weaver et al. (2021) <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008755>.

Authors:Davis Weaver [aut, cre]

crosstalkr_1.0.5.tar.gz
crosstalkr_1.0.5.tar.gz(r-4.5-noble)crosstalkr_1.0.5.tar.gz(r-4.4-noble)
crosstalkr_1.0.5.tgz(r-4.4-emscripten)crosstalkr_1.0.5.tgz(r-4.3-emscripten)
crosstalkr.pdf |crosstalkr.html✨
crosstalkr/json (API)

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

Peer review:

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 7 scripts 654 downloads 34 exports 122 dependencies

Last updated 6 months agofrom:afb1affa18. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-linux-x86_64OKNov 14 2024

Exports:add_valueas_gene_symbolbootstrap_nullcalc_dnp_icalc_npcalc_np_allcalc_np_icombine_nullcompute_crosstalkcompute_dnpcompute_npcompute_null_dnpcrosstalk_subgraphdist_calcexperiment_breakoutfinal_combineget_random_graphgfiltergfilter.ctgfilter.igraph_methodgfilter.npgfilter.valueload_ppinode_repressionnorm_colsumplot_ctppi_intersectionppi_unionprep_biogridprep_stringdbsparseRWRsupported_speciestidy_expressionto_taxon_id

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcaToolschronclicliprcodetoolscolorspacecpp11crayoncurlDBIDelayedArraydoParalleldplyrensembldbfansifarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgsubfngtablegtoolshashhmshttrigraphIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotrixplyrpngprettyunitsprogressProtGenericsprotopurrrR6RColorBrewerRcppRCurlreadrrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraysqldfSTRINGdbstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryamlzlibbioc

Using crosstalkr for drug target identification

Rendered fromcrosstalkr_vignette.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2023-05-18
Started: 2021-08-16

Readme and manuals

Help Manual

Help pageTopics
attach expression values from user-provided expression vector to graph.add_expression
Attach a generic user-provided value to graphadd_value
Convert from most other representations of gene name to gene.symbolas_gene_symbol
Bootstrap null distribution for RWRbootstrap_null
helper function to calculate dnp for one samplecalc_dnp_i
calculate network potential for one node.calc_np
function to calculate the network potential for each protein in a user-provided vector - cpp internal versioncalc_np_all
function to calculate the network potential for each protein in a user-provided vectorcalc_np_all_legacy
helper function to calculate np for one samplecalc_np_i
Check to make sure incoming object is a valid crosstalk df.check_crosstalk
.combine function for compute_null foreach looping structurecombine_null
Identify proteins with a statistically significant relationship to user-provided seeds.compute_crosstalk
main function to compute delta np for every gene in a given dataframe - assumes compute_np has already been run for a given datasetcompute_dnp
main function to compute np from a user-provided expression matrix.compute_np
function to compute null distribution of dnpcompute_null_dnp
Helper function to generate subgraph from crosstalk_df output of 'compute_crosstalk'crosstalk_subgraph
crosstalkr: A package for the identification of functionally relevant subnetworks from high-dimensional omics data.crosstalkr
Determine which format of gene is used to specify by user-defined seed proteinsdetect_inputtype
Internal function that computes the mean/stdev for each gene from a wide-format data frame.dist_calc
Determine if ensembl id is a Protein, gene, or transcript_idensembl_type
helper function to split experiment names into constituent partsexperiment_breakout
Function to calculate the network potential for vertices vfcalc_np_all
final .combine function to run in compute_null_dnp foreach looping structurefinal_combine
Internal function that computes the mean/stdev for each gene from a wide-format data frame.final_dist_calc
function to get graph neighbors (along with their expression values) for a given gene in a given network gget_neighbors
Helper function for compute_null_dnp - returns a graph with randomly permuted edges.get_random_graph
Helper function for compute_null_dnp - returns the top n genes by dnp for each sampleget_topn
Generic function to filter either an igraph object or a PPI networkgfilter
Method to filter the graph based on parameters passed to compute_crosstalkgfilter.ct
Method to filter graph based on any igraph method that scores verticies.gfilter.igraph_method
Method to filter graph based on network potential values.gfilter.np
Method to filter graph based on user provided valuegfilter.value
Determine if a character vector contains ensembl gene_idsis_ensembl
Determine if a character vector contains entrez gene_idsis_entrez
Helper function to load requested PPI w/ parametersload_ppi
Identify random sets of seeds with similar degree distribution to parent seed proteinsmatch_seeds
Function to eliminate a node from a network g and calculate the change in some measure of network statenode_repression
Function to normalize adjacency matrix by dividing each value by the colsum.norm_colsum
Plot subnetwork identified using the compute_crosstalk functionplot_ct
Function to allow users to choose the intersection of stringdb and biogrid Only works with the human PPI. min_score parameter only applies to strindbppi_intersection
Function to allow users to choose the union of stringdb and biogrid Only works with the human PPI. min_score parameter only applies to strindbppi_union
Prepare biogrid for use in analysesprep_biogrid
Prepare Stringdb for use in analysesprep_stringdb
Perform random walk with repeats on a sparse matrixsparseRWR
returns a dataframe with information on supported speciessupported_species
helper function to convert expression matrix to tidy dataframe (if not already)tidy_expression
helper to convert user-inputs to ncbi reference taxonomy.to_taxon_id