Cellmap analysis modules written in GO. This was built with GO modules.
git clone https://github.com/knightjdr/cmgo.git
cd cmgo
go build ./...
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.
Modules for generating files for upload and query file processing.
- folder
analysis/dbgenes
Generates a txt file of official genes used for SAINT
- folder
assessment/localization/recovered
Get the genes assigned to a specific compartment by GO and report on those seen from a list of genes.
- folder
assessment/countgo
Count the number of genes with a GO term specified by the supplied namespace.
- folder
assessment/go
Perform GO analysis on baits in a SAINT file
- 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.
- folder
assessment/hydropathy
Measures the average hydropathy of proteins in a SAINT file and a BioPlex dataset
- folder
assessment/localization/evaluate
Report on which localizations are previously known.
- folder
assessment/localization/prediction
Assign a prediction score for every prey localized by NMF or SAFE
- folder
assessment/transmembrane
Information about the transmembrane proteins residing between two NMF compartments.
- folder
assessment/controls/preys
Output statistics on prey proteins in controls using SAINT input files.
Modules for calculating term enrichment in compartments and lists.
- folder
enrichment/genes
Perform a g:Profiler enrichment on a list of genes
- folder
enrichment/heatmap
Creates a heat map visualizing region (domain/motif) fold enrichment (scaled to Log2) across NMF or SAFE compartments.
- 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.
- folder
interaction/rankaverage
Calculates the average bait interaction rank for a list of preys.
- folder
interaction/rankmetrics
Calculates metrics for preys by interaction rank, including expression level, number of lysines and turnover rate.
- folder
lba/correlation
Calculate correlation between LBA profiles and output Cytoscape formatted file for viewing network.
- folder
lba/enrichment
Enrichment performs GO enrichments of preys from a SAINT file using LBA.
- folder
lba/localize
Localize preys based on enriched terms for LBA
- folder
assessment/localization/nmfsafe
Check concordance between NMF and SAFE localizations
Modules for creating networks
Create an svg network for NMF or SAFE
Convert a tSNE coordinate system into a .cyjs file for Cytoscape
Modules for NMF (and related) analysis.
- folder
nmf/moonlighting
Calculates a moonlighting score for preys in an NMF basis matrix
- 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.
- folder
nmf/subset
Subset an NMF basis (prey) matrix to only include preys enriched in specified compartments.
- 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
Modules for comparing cell map compartments.
- 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.
- 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.
- folder
organelle/shared
Takes two lists of proteins and outputs metrics on the regions (domains/motifs) shared between common preys.
Modules for prey-prey analysis
- folder
preyprey/subset
Subset a ProHits-viz interactive file to grab a cluster
SAINT file summaries and information
- folder
summary/crapome
Generates a CRAPome matrix from SAINT input files
- folder
summary/notsignificant
Generates a list of preys that were not significant with any bait in a SAINT file.
- 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