Directories
¶
| Path | Synopsis |
|---|---|
|
analysis
|
|
|
dbgenes
Package dbgenes generates a list of genes in sequence database
|
Package dbgenes generates a list of genes in sequence database |
|
assessment
|
|
|
bait/gradient
Package gradient draws a similarity gradient for baits.
|
Package gradient draws a similarity gradient for baits. |
|
controls/preys
Package preys outputs statistics on prey proteins in controls.
|
Package preys outputs statistics on prey proteins in controls. |
|
countgo
Package countgo count the number of genes with a GO term.
|
Package countgo count the number of genes with a GO term. |
|
goenrich
Package goenrich finds enriched GO terms via gProfiler
|
Package goenrich finds enriched GO terms via gProfiler |
|
hydropathy
Package hydropathy calculates the average hydropathy of proteins sequences
|
Package hydropathy calculates the average hydropathy of proteins sequences |
|
localization/evaluate
Package evaluate localizes preys using LBA
|
Package evaluate localizes preys using LBA |
|
localization/nmfsafe
Package nmfsafe checks NMF and SAFE localizations for agreement.
|
Package nmfsafe checks NMF and SAFE localizations for agreement. |
|
localization/prediction
Package prediction calculates a prediction score for each prey.
|
Package prediction calculates a prediction score for each prey. |
|
localization/recovered
Package recovered reports the number of genes seen in a specific compartment.
|
Package recovered reports the number of genes seen in a specific compartment. |
|
transmembrane
Package transmembrane reports the orientation evidence for transmembrane preys.
|
Package transmembrane reports the orientation evidence for transmembrane preys. |
|
enrichment
|
|
|
genes
Package genes performs a GO enrichment on a list of genes.
|
Package genes performs a GO enrichment on a list of genes. |
|
heatmap
Package heatmap creates a heat map to display enriched regions across compartments.
|
Package heatmap creates a heat map to display enriched regions across compartments. |
|
interaction
|
|
|
knownbyrank
Package knownbyrank calculates the proportion of known interactors for the Nth best prey across baits in a SAINT report
|
Package knownbyrank calculates the proportion of known interactors for the Nth best prey across baits in a SAINT report |
|
rankaverage
Package rankaverage calculates the average interaction ranks for supplied prey list
|
Package rankaverage calculates the average interaction ranks for supplied prey list |
|
rankmetrics
Package rankmetrics calculates prey metrics for each prey interaction rank.
|
Package rankmetrics calculates prey metrics for each prey interaction rank. |
|
Package lba is for localizing prey genes.
|
Package lba is for localizing prey genes. |
|
enrichment
Package enrichment performs GO enrichments for LBA.
|
Package enrichment performs GO enrichments for LBA. |
|
localize
Package localize localizes preys using LBA
|
Package localize localizes preys using LBA |
|
network
|
|
|
correlation
Package correlation creates files for visualizing LBA as a correlation network.
|
Package correlation creates files for visualizing LBA as a correlation network. |
|
matrix
Package matrix creates files for visualizing LBA as a correlation network.
|
Package matrix creates files for visualizing LBA as a correlation network. |
|
svg
Package svg creates a network in svg format from NMF or SAFE data.
|
Package svg creates a network in svg format from NMF or SAFE data. |
|
tsnecytoscape
Package tsnecytoscape generates a Cytoscape network from t-SNE coordinates.
|
Package tsnecytoscape generates a Cytoscape network from t-SNE coordinates. |
|
nmf
|
|
|
moonlighting
Package moonlighting scores preys localized by NMF for moonlighting in more than one compartment
|
Package moonlighting scores preys localized by NMF for moonlighting in more than one compartment |
|
robustness
Package robustness assesses the sensitivity of NMF rank assignments
|
Package robustness assesses the sensitivity of NMF rank assignments |
|
subset
Package subset filters an NMF basis (prey) matrix to only include preys enriched all specified rank.
|
Package subset filters an NMF basis (prey) matrix to only include preys enriched all specified rank. |
|
uv
Package uv validates the localizations of prey genes not used for defining NMF ranks
|
Package uv validates the localizations of prey genes not used for defining NMF ranks |
|
isolation
Package isolation calculates percent isolation of each NMF compartment.
|
Package isolation calculates percent isolation of each NMF compartment. |
|
overlap
Package overlap calculates overlap metrics between two lists of proteins
|
Package overlap calculates overlap metrics between two lists of proteins |
|
shared
Package shared outputs metrics on the regions found in preys shared by two lists of proteins
|
Package shared outputs metrics on the regions found in preys shared by two lists of proteins |
|
pkg
|
|
|
cluster
Package cluster clusters a matrix
|
Package cluster clusters a matrix |
|
function
Package function returns functions defined from input arguments
|
Package function returns functions defined from input arguments |
|
image/file
Package file has methods for opening and writing to a file for creating images
|
Package file has methods for opening and writing to a file for creating images |
|
image/svg/heatmap
Package heatmap creates svg files for various image types.
|
Package heatmap creates svg files for various image types. |
|
localization
Package localization contains functions for assessing localizations
|
Package localization contains functions for assessing localizations |
|
nmf
Package nmf implements common functions for NMF analysis.
|
Package nmf implements common functions for NMF analysis. |
|
read/bioplex
Package bioplex reads a Bioplex interaction file
|
Package bioplex reads a Bioplex interaction file |
|
read/csv
Package csv reads a csv file
|
Package csv reads a csv file |
|
read/database
Package database reads a fasta database to an array.
|
Package database reads a fasta database to an array. |
|
read/geneontology
Package geneontology contains functions for reading and parsing Gene Ontology (GO) files.
|
Package geneontology contains functions for reading and parsing Gene Ontology (GO) files. |
|
read/interactions
Package interactions reads interactions from BioGRID and/or Intact
|
Package interactions reads interactions from BioGRID and/or Intact |
|
read/matrix
Package matrix reads matrix from txt file.
|
Package matrix reads matrix from txt file. |
|
read/nmf
Package nmf reads NMF output files and assesses localizations
|
Package nmf reads NMF output files and assesses localizations |
|
read/pfam
Package pfam reads domain and motif information from a file.
|
Package pfam reads domain and motif information from a file. |
|
read/safe
Package safe read SAFE output files
|
Package safe read SAFE output files |
|
read/saint
Package saint reads and parses SAINT-related files.
|
Package saint reads and parses SAINT-related files. |
|
read/tsne
Package tsne reads t-SNE coordinate file.
|
Package tsne reads t-SNE coordinate file. |
|
read/uniprot
Package uniprot reads a uniprot database.
|
Package uniprot reads a uniprot database. |
|
preyprey
|
|
|
subset
Package subset gets a cluster from a prey-prey interactive file.
|
Package subset gets a cluster from a prey-prey interactive file. |
|
summary
|
|
|
crapome
Package crapome generates a CRAPome matrix from SAINT input files.
|
Package crapome generates a CRAPome matrix from SAINT input files. |
|
notsignificant
Package notsignificant outputs non significant preys
|
Package notsignificant outputs non significant preys |
Click to show internal directories.
Click to hide internal directories.