Package index • CroCoNet

All functions

POU5F1_target_conservation: Cross-species conservation measures of the target genes in the POU5F1 module
addDirectionality(): Add directionality of interactions
applyPower(): Apply soft-thresholding
assignInitialModules(): Assign initial modules
calculateEdgeDivergence(): Calculate the divergence of intramodular edges
calculateEigengenes(): Calculate module eigengenes
calculatePresStats(): Calculate preservation statistics
calculateTreeStats(): Calculate tree statistics across all modules
comparePresStats(): Compare preservation statistics
consensus_network: Consensus network
convertPresToDist(): Convert preservation statistics to distances across all modules
convertToDT(): Convert a list of igraphs to a list of data tables
convertToGraph(): Convert a list of data frames to a list of igraphs
createConsensus(): Create consensus network
createRandomModules(): Create random modules
dist: Distance measures of the pruned modules
dist_jk: Distance measures of the original and jackknifed pruned modules
eigengenes: Eigengenes
eigengenes_per_species: Eigengenes per species
filterModuleTrees(): Filter modules based on their tree representations
findConservedDivergedModules(): Find conserved and diverged modules
findConservedDivergedTargets(): Find conserved and diverged target genes within a module
fitTreeStatsLm(): Fit (weighted) linear model between tree-based statistics
genes: All genes
getRegulators(): Get transcriptional regulators
getTreeDf(): Convert a tree to a data frame
gtf_list: List of genomic annotations
image_TRs: IMAGE transcriptional regulators
initial_modules: Initial modules
jaspar_core_TRs: JASPAR 2024 vertebrate core transcriptional regulators
jaspar_unvalidated_TRs: JASPAR 2024 unvalidated transcriptional regulators
lm_overall: Linear model for the characterization of overall module conservation
loadNetworks(): Load networks as a list of igraph objects
module_conservation_overall: Cross-species conservation measures per module
network_list: List of networks
network_list_raw: List of raw networks
normalizeEdgeWeights(): Normalize edge weights between 0 and 1
plotConservedDivergedModules(): Plot module conservation
plotConservedDivergedTargets(): Plot target conservation
plotDistMats(): Plot the distance matrices of replicates based on module connectivity patterns
plotEigengeneHeatmap(): Plot module eigengenes as a heatmap
plotEigengenesAlongPseudotime(): Plot module eigengenes along a pseudotime trajectory
plotEigengenesViolin(): Plot eigengene distributions per cell type and species
plotExprAlongPseudotime(): Plot expression profiles along a pseudotime trajectory
plotExprHeatmap(): Plot expression profiles as a heatmap
plotExprViolin(): Plot expression distributions per cell type and species
plotModuleSizeDistribution(): Plot the distribution of module sizes
plotNetworks(): Plot the networks of modules
plotPresStatDistributions(): Plot the distributions of preservation statistics
plotPresStats(): Plot cross-species VS within-species preservation statistics per species pair
plotSumEigengeneHeatmap(): Plot summarized eigengenes as a heatmap
plotSumEigengenesLine(): Plot summarized eigengenes as a line plot
plotSumExprHeatmap(): Plot summarized expression profiles as a heatmap
plotSumExprLine(): Plot summarized expression profiles as a line plot
plotTreeStatDistributions(): Plot the distributions of tree-based statistics
plotTreeStats(): Plot tree-based statistics against each other
plotTrees(): Plot the tree representations of modules
pres_stats: Preservation statistics of the pruned modules
pres_stats_jk: Preservation statistics of the original and jackknifed pruned modules
pruneModules(): Prune modules
pruneModules_UIK_adj(): Prune modules based on the regulator-target adjacencies using dynamic filtering
pruneModules_UIK_adj_kIM(): Prune modules based on the regulator-target adjacencies and intramodular connectivities using dynamic filtering
pruneModules_topN(): Prune modules based on the regulator-target adjacencies by keeping a fixed number of top targets
pruned_modules: Pruned modules
random_dist_jk: Distance measures of the the original and jackknifed random modules
random_modules: Random modules
random_pres_stats: Preservation statistics of the random modules
random_pres_stats_jk: Preservation statistics of the the original and jackknifed random modules
random_tree_stats: Tree-based statistics of the random modules
random_tree_stats_jk: Tree-based statistics of the original and jackknifed random modules
random_trees_jk: Trees of the original and jackknifed random modules
reconstructTrees(): Reconstruct trees across all modules
regulators: Transcriptional regulators
removeOverlappingGenePairs(): Remove gene pairs with overlapping annotations
replicate2species: Replicate-species conversion
scaleFreeFitRSquared(): Calculate R2 value of the scale-free model fit for the provided connectivities
sce: SCE object of the primate neural differentiation dataset
selectPower(): Select power for scale-free transfrmation
summarizeJackknifeStats(): Summarize jackknife statistics
summarizeStat(): Summarize values of a statistic
testPowers(): Test soft-thresholding power values
tree: Phylogenetic tree
tree_stats: Tree-based statistics of the pruned modules
tree_stats_jk: Tree-based statistics of the original and jackknifed pruned modules
trees: Trees of the pruned modules
trees_jk: Trees of the original and jackknifed pruned modules