cmgo

module
Version: v0.0.0-...-e7b93c9 Latest Latest
Warning

This package is not in the latest version of its module.

Go to latest
Published: Jul 27, 2021 License: MIT

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

  1. CRAPome matrix
  • module: summary-crapome
  • filename: crapome-matrix-v1.txt
  • destination: client/resources/downloads
  1. preys detected in samples that are not significant
  • module: summary-notsignificant
  • filename: not-significant-v1.txt
  • destination: client/resources/downloads
  1. sequence database
  • download FASTA database from ProHits
  • filename: sequence-database-v1.txt
  • destination: client/resources/downloads
  1. genes in database
  • module: analysis-dbgenes
  • filename: v1_dbgenes.txt
  • destination: api/app/data/genes

Directories

Path Synopsis
cmd
pkg
correlation
Package correlation calculates the correlation coefficient between two slices.
Package correlation calculates the correlation coefficient between two slices.
filter
Package filter contains filtering functions for maps.
Package filter contains filtering functions for maps.
flags
Package flags handles flag parsing
Package flags handles flag parsing
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
gene
Package gene implements methods for mapping gene IDs
Package gene implements methods for mapping gene IDs
gprofiler
Package gprofiler performs and term enrichment at g:Profiler
Package gprofiler performs and term enrichment at g:Profiler
mapfunc
Package mapfunc contains methods for manipulating maps.
Package mapfunc contains methods for manipulating maps.
math
Package math defines common math operations
Package math defines common math operations
matrix
Package matrix contains methods for operating on matrices.
Package matrix contains methods for operating on matrices.
pfam
Package pfam will get regions for a list of UniProt IDs.
Package pfam will get regions for a list of UniProt IDs.
random
Package random contains functions for operations with random effects.
Package random contains functions for operations with random effects.
rbo
Package rbo calculates the rank biased overlap between ordered lists
Package rbo calculates the rank biased overlap between ordered lists
slice
Package slice contains methods for slice conversion and modification
Package slice contains methods for slice conversion and modification
sort
Package sort contains sorting functions
Package sort contains sorting functions
strfunc
Package strfunc contains functions for handling and modifying strings
Package strfunc contains functions for handling and modifying strings
uniprot
Package uniprot will get uniprot entries for a list of IDs.
Package uniprot will get uniprot entries for a list of IDs.
internal
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
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.
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.
assessment/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.
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
Package rankaverage calculates the average interaction ranks for supplied prey list
interaction/rankmetrics
Package rankmetrics calculates prey metrics for each prey interaction rank.
Package rankmetrics calculates prey metrics for each prey interaction rank.
lba
Package lba is for localizing prey genes.
Package lba is for localizing prey genes.
lba/enrichment
Package enrichment performs GO enrichments for LBA.
Package enrichment performs GO enrichments for LBA.
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.
network/matrix
Package matrix creates files for visualizing LBA as a correlation network.
Package matrix creates files for visualizing LBA as a correlation network.
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.
network/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
nmf/robustness
Package robustness assesses the sensitivity of NMF rank assignments
Package robustness assesses the sensitivity of NMF rank assignments
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.
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
organelle/isolation
Package isolation calculates percent isolation of each NMF compartment.
Package isolation calculates percent isolation of each NMF compartment.
organelle/overlap
Package overlap calculates overlap metrics between two lists of proteins
Package overlap calculates overlap metrics between two lists of proteins
organelle/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
pkg/function
Package function returns functions defined from input arguments
Package function returns functions defined from input arguments
pkg/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
pkg/image/svg/heatmap
Package heatmap creates svg files for various image types.
Package heatmap creates svg files for various image types.
pkg/localization
Package localization contains functions for assessing localizations
Package localization contains functions for assessing localizations
pkg/nmf
Package nmf implements common functions for NMF analysis.
Package nmf implements common functions for NMF analysis.
pkg/read/bioplex
Package bioplex reads a Bioplex interaction file
Package bioplex reads a Bioplex interaction file
pkg/read/csv
Package csv reads a csv file
Package csv reads a csv file
pkg/read/database
Package database reads a fasta database to an array.
Package database reads a fasta database to an array.
pkg/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.
pkg/read/interactions
Package interactions reads interactions from BioGRID and/or Intact
Package interactions reads interactions from BioGRID and/or Intact
pkg/read/matrix
Package matrix reads matrix from txt file.
Package matrix reads matrix from txt file.
pkg/read/nmf
Package nmf reads NMF output files and assesses localizations
Package nmf reads NMF output files and assesses localizations
pkg/read/pfam
Package pfam reads domain and motif information from a file.
Package pfam reads domain and motif information from a file.
pkg/read/safe
Package safe read SAFE output files
Package safe read SAFE output files
pkg/read/saint
Package saint reads and parses SAINT-related files.
Package saint reads and parses SAINT-related files.
pkg/read/tsne
Package tsne reads t-SNE coordinate file.
Package tsne reads t-SNE coordinate file.
pkg/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.
summary/notsignificant
Package notsignificant outputs non significant preys
Package notsignificant outputs non significant preys

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL