README
¶
Cellmap analysis modules
Cellmap analysis modules written in GO. This was built with GO modules.
Build
git clone https://github.com/knightjdr/cmgo.git
cd cmgo
go build ./...
Run an analysis module
An options file in JSON format can be used to define run time arguments. Arguments can also be supplied on the command line (these will override corresponding arguments specified in the options file).
A module name must always be supplied for analysis.
cmgo -options="config.json" -module="module-name"
Module specific parameters can be found in the README files in the corresponding folder.
Analysis
Module name
Modules for generating files for upload and query file processing.
Module name: analysis-dbgenes
- folder
analysis/dbgenes
Generates a txt file of official genes used for SAINT
Assessment
Module name: assessment-compartment-recovered
- folder
assessment/localization/recovered
Get the genes assigned to a specific compartment by GO and report on those seen from a list of genes.
Module name: assessment-countgo
- folder
assessment/countgo
Count the number of genes with a GO term specified by the supplied namespace.
Module name: assessment-go
- folder
assessment/go
Perform GO analysis on baits in a SAINT file
Module name: bait-gradient
- folder
assessment/bait/gradient
Takes an ordered bait list and expected localizations for the baits and outputs a gradient showing adjacent bait similarity: black if the two adjacent baits share an expected localization, grey if only one does and white otherwise.
Module name: assessment-hydropathy
- folder
assessment/hydropathy
Measures the average hydropathy of proteins in a SAINT file and a BioPlex dataset
Module name: assessment-localization
- folder
assessment/localization/evaluate
Report on which localizations are previously known.
Module name: assessment-prediction
- folder
assessment/localization/prediction
Assign a prediction score for every prey localized by NMF or SAFE
Module name: assessment-transmembrane
- folder
assessment/transmembrane
Information about the transmembrane proteins residing between two NMF compartments.
Control
- folder
assessment/controls/preys
Module name: control-preys
Output statistics on prey proteins in controls using SAINT input files.
Enrichment
Modules for calculating term enrichment in compartments and lists.
Module name: enrichment-genes
- folder
enrichment/genes
Perform a g:Profiler enrichment on a list of genes
Module name: enrichment-heatmap
- folder
enrichment/heatmap
Creates a heat map visualizing region (domain/motif) fold enrichment (scaled to Log2) across NMF or SAFE compartments.
Interactors
Module name: interaction-knownbyrank
- folder
interaction/knownbyrank
Calculates the proportion of known interactors for the Nth best prey across all baits in a SAINT report. Prey spectral counts are control subtracted and length normalized to determine their rank.
Module name: interaction-rankaverage
- folder
interaction/rankaverage
Calculates the average bait interaction rank for a list of preys.
Module name: interaction-rankmetrics
- folder
interaction/rankmetrics
Calculates metrics for preys by interaction rank, including expression level, number of lysines and turnover rate.
LBA
Module name: lba-correlation
- folder
lba/correlation
Calculate correlation between LBA profiles and output Cytoscape formatted file for viewing network.
Module name: lba-enrichment
- folder
lba/enrichment
Enrichment performs GO enrichments of preys from a SAINT file using LBA.
Module name: lba-localize
- folder
lba/localize
Localize preys based on enriched terms for LBA
Module name: nmf-v-safe
- folder
assessment/localization/nmfsafe
Check concordance between NMF and SAFE localizations
Network
Modules for creating networks
Module name: network-svg
Create an svg network for NMF or SAFE
Module name: network-tsnecytoscape
Convert a tSNE coordinate system into a .cyjs file for Cytoscape
NMF
Modules for NMF (and related) analysis.
Module name: nmf-moonlighting
- folder
nmf/moonlighting
Calculates a moonlighting score for preys in an NMF basis matrix
Module name: nmf-robustness
- folder
nmf/robustness
Evaluates how robust each rank's GO terms are based on the genes used to define it. It will first define the rank by performing a GO enrichment using at most maxGenesPerRank, and then repeat this when using 90%, 80%... of the maxGenesPerRank. For each evaluation it will calculate the RBD between the list generated for maxGenesPerRank and the fractional list.
Module name: nmf-subset
- folder
nmf/subset
Subset an NMF basis (prey) matrix to only include preys enriched in specified compartments.
Module name: nmf-uv
- folder
nmf/uv
For all prey genes not used to define an NMF rank, it calculates what proportion are being assigned to a previously known localization. UV: unused validation
Organelle comparison
Modules for comparing cell map compartments.
Module name: organelle-isolation
- folder
organelle/isolation
Calculates how isolated an NMF compartment is, i.e. for genes localizing to the compartment the number of edges between members of the compartment relative to the number of edges to proteins outside the compartment.
Module name: organelle-overlap
- folder
organelle/overlap
Takes two lists of proteins and a txt file with similarity scores between proteins and outputs metrics on the similarity within and between the lists.
Module name: organelle-sharedregion
- folder
organelle/shared
Takes two lists of proteins and outputs metrics on the regions (domains/motifs) shared between common preys.
Prey prey
Modules for prey-prey analysis
Module name: preyprey-subset
- folder
preyprey/subset
Subset a ProHits-viz interactive file to grab a cluster
Summary
SAINT file summaries and information
Module name: summary-crapome
- folder
summary/crapome
Generates a CRAPome matrix from SAINT input files
Module name: summary-notsignificant
- folder
summary/notsignificant
Generates a list of preys that were not significant with any bait in a SAINT file.
Files for website
- CRAPome matrix
- module:
summary-crapome - filename:
crapome-matrix-v1.txt - destination: client/resources/downloads
- preys detected in samples that are not significant
- module:
summary-notsignificant - filename:
not-significant-v1.txt - destination: client/resources/downloads
- sequence database
- download FASTA database from ProHits
- filename:
sequence-database-v1.txt - destination: client/resources/downloads
- genes in database
- module:
analysis-dbgenes - filename:
v1_dbgenes.txt - destination: api/app/data/genes
Directories
¶
| Path | Synopsis |
|---|---|
|
cmd
|
|
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internal
|
|
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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. |
|
assessment/controls/preys
Package preys outputs statistics on prey proteins in controls.
|
Package preys outputs statistics on prey proteins in controls. |
|
assessment/countgo
Package countgo count the number of genes with a GO term.
|
Package countgo count the number of genes with a GO term. |
|
assessment/goenrich
Package goenrich finds enriched GO terms via gProfiler
|
Package goenrich finds enriched GO terms via gProfiler |
|
assessment/hydropathy
Package hydropathy calculates the average hydropathy of proteins sequences
|
Package hydropathy calculates the average hydropathy of proteins sequences |
|
assessment/localization/evaluate
Package evaluate localizes preys using LBA
|
Package evaluate localizes preys using LBA |
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assessment/localization/nmfsafe
Package nmfsafe checks NMF and SAFE localizations for agreement.
|
Package nmfsafe checks NMF and SAFE localizations for agreement. |
|
assessment/localization/prediction
Package prediction calculates a prediction score for each prey.
|
Package prediction calculates a prediction score for each prey. |
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assessment/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. |
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assessment/transmembrane
Package transmembrane reports the orientation evidence for transmembrane preys.
|
Package transmembrane reports the orientation evidence for transmembrane preys. |
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enrichment/genes
Package genes performs a GO enrichment on a list of genes.
|
Package genes performs a GO enrichment on a list of genes. |
|
enrichment/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 |
|
interaction/rankaverage
Package rankaverage calculates the average interaction ranks for supplied prey list
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Package rankaverage calculates the average interaction ranks for supplied prey list |
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interaction/rankmetrics
Package rankmetrics calculates prey metrics for each prey interaction rank.
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Package rankmetrics calculates prey metrics for each prey interaction rank. |
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lba
Package lba is for localizing prey genes.
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Package lba is for localizing prey genes. |
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lba/enrichment
Package enrichment performs GO enrichments for LBA.
|
Package enrichment performs GO enrichments for LBA. |
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lba/localize
Package localize localizes preys using LBA
|
Package localize localizes preys using LBA |
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network/correlation
Package correlation creates files for visualizing LBA as a correlation network.
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Package correlation creates files for visualizing LBA as a correlation network. |
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network/matrix
Package matrix creates files for visualizing LBA as a correlation network.
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Package matrix creates files for visualizing LBA as a correlation network. |
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network/svg
Package svg creates a network in svg format from NMF or SAFE data.
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Package svg creates a network in svg format from NMF or SAFE data. |
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network/tsnecytoscape
Package tsnecytoscape generates a Cytoscape network from t-SNE coordinates.
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Package tsnecytoscape generates a Cytoscape network from t-SNE coordinates. |
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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 |
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nmf/robustness
Package robustness assesses the sensitivity of NMF rank assignments
|
Package robustness assesses the sensitivity of NMF rank assignments |
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nmf/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. |
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nmf/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 |
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organelle/isolation
Package isolation calculates percent isolation of each NMF compartment.
|
Package isolation calculates percent isolation of each NMF compartment. |
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organelle/overlap
Package overlap calculates overlap metrics between two lists of proteins
|
Package overlap calculates overlap metrics between two lists of proteins |
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organelle/shared
Package shared outputs metrics on the regions found in preys shared by two lists of proteins
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Package shared outputs metrics on the regions found in preys shared by two lists of proteins |
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pkg/cluster
Package cluster clusters a matrix
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Package cluster clusters a matrix |
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pkg/function
Package function returns functions defined from input arguments
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Package function returns functions defined from input arguments |
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pkg/image/file
Package file has methods for opening and writing to a file for creating images
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Package file has methods for opening and writing to a file for creating images |
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pkg/image/svg/heatmap
Package heatmap creates svg files for various image types.
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Package heatmap creates svg files for various image types. |
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pkg/localization
Package localization contains functions for assessing localizations
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Package localization contains functions for assessing localizations |
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pkg/nmf
Package nmf implements common functions for NMF analysis.
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Package nmf implements common functions for NMF analysis. |
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pkg/read/bioplex
Package bioplex reads a Bioplex interaction file
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Package bioplex reads a Bioplex interaction file |
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pkg/read/csv
Package csv reads a csv file
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Package csv reads a csv file |
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pkg/read/database
Package database reads a fasta database to an array.
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Package database reads a fasta database to an array. |
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pkg/read/geneontology
Package geneontology contains functions for reading and parsing Gene Ontology (GO) files.
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Package geneontology contains functions for reading and parsing Gene Ontology (GO) files. |
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pkg/read/interactions
Package interactions reads interactions from BioGRID and/or Intact
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Package interactions reads interactions from BioGRID and/or Intact |
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pkg/read/matrix
Package matrix reads matrix from txt file.
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Package matrix reads matrix from txt file. |
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pkg/read/nmf
Package nmf reads NMF output files and assesses localizations
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Package nmf reads NMF output files and assesses localizations |
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pkg/read/pfam
Package pfam reads domain and motif information from a file.
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Package pfam reads domain and motif information from a file. |
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pkg/read/safe
Package safe read SAFE output files
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Package safe read SAFE output files |
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pkg/read/saint
Package saint reads and parses SAINT-related files.
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Package saint reads and parses SAINT-related files. |
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pkg/read/tsne
Package tsne reads t-SNE coordinate file.
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Package tsne reads t-SNE coordinate file. |
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pkg/read/uniprot
Package uniprot reads a uniprot database.
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Package uniprot reads a uniprot database. |
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preyprey/subset
Package subset gets a cluster from a prey-prey interactive file.
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Package subset gets a cluster from a prey-prey interactive file. |
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summary/crapome
Package crapome generates a CRAPome matrix from SAINT input files.
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Package crapome generates a CRAPome matrix from SAINT input files. |
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summary/notsignificant
Package notsignificant outputs non significant preys
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Package notsignificant outputs non significant preys |
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pkg
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correlation
Package correlation calculates the correlation coefficient between two slices.
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Package correlation calculates the correlation coefficient between two slices. |
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filter
Package filter contains filtering functions for maps.
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Package filter contains filtering functions for maps. |
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flags
Package flags handles flag parsing
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Package flags handles flag parsing |
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fs
Package fs creates a filesystem to use (for easy mocking) This replaces most of the filesystem and io methods from os and io
|
Package fs creates a filesystem to use (for easy mocking) This replaces most of the filesystem and io methods from os and io |
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gene
Package gene implements methods for mapping gene IDs
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Package gene implements methods for mapping gene IDs |
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gprofiler
Package gprofiler performs and term enrichment at g:Profiler
|
Package gprofiler performs and term enrichment at g:Profiler |
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mapfunc
Package mapfunc contains methods for manipulating maps.
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Package mapfunc contains methods for manipulating maps. |
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math
Package math defines common math operations
|
Package math defines common math operations |
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matrix
Package matrix contains methods for operating on matrices.
|
Package matrix contains methods for operating on matrices. |
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pfam
Package pfam will get regions for a list of UniProt IDs.
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Package pfam will get regions for a list of UniProt IDs. |
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random
Package random contains functions for operations with random effects.
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Package random contains functions for operations with random effects. |
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rbo
Package rbo calculates the rank biased overlap between ordered lists
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Package rbo calculates the rank biased overlap between ordered lists |
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slice
Package slice contains methods for slice conversion and modification
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Package slice contains methods for slice conversion and modification |
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sort
Package sort contains sorting functions
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Package sort contains sorting functions |
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strfunc
Package strfunc contains functions for handling and modifying strings
|
Package strfunc contains functions for handling and modifying strings |
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uniprot
Package uniprot will get uniprot entries for a list of IDs.
|
Package uniprot will get uniprot entries for a list of IDs. |