MetamapsDB
Network Analysis of Metabolic Pathways and Gene Based Assemblies in Metagenomics
Functions for path based queries against 'Omics' < https://github.com/etheleon/omics-neo4j-container>, a 'NEO4J' < https://neo4j.com/> database populated with data from metagenomic surveys and their accompanying metabolic and taxonomic annotations.
MetamapsDB
R package for querying integrated -omics database.
Introduction
MetamapsDB is a R package used for interfacing with such a database for
- Gene centric queries
- Analyses of Integrated^ Microbiome datasets
^ Genomic and Transcriptomic
It is the final step of the 5 preprocessing steps used in carrying out our gene centric pipeline. (Unpublished)
- Annotation DIAMOND - Labelling of short reads using, blastX-like against NR protein database (more for functional)
- Binning MEGAN6 CE - Functional (KEGG) binning of NGS short reads based on labels
- Bin-based Assembly NEWBLER - Gene Centric OLC Assembly of functional bins / KEGG Orthologs
- Annotation DIAMOND - Labelling (round2) more for taxonomic annotation
- MEGAN6 CE - Taxonomic binning of contigs based on labels
- Gene centric analyses pAss -
- Identify Maximum Diversity Region (MDR)
- Remove known KOs which fail process
- Diversity analysis (gene count)
- 31 Single Copy Genes
- ID genera which are indistinguishable due to sequence conservation
- Diversity analysis (gene count)
- mapBlat - Maps (using BLAT) gDNA and rRNA short onto
- the contigs
- just the MDR Region
Mentioned Packages
OMICS
Docker wrapper for generating a KEGG + Taxnoomy + Contig neo4j graph database
MapBloat
R package for mapping reads onto contigs/MDR using Blat
Usage
Functions
| Function | Description |
|---|---|
| connect | Connects with Neo4J database |
| dbquery | Sends query to Neo4J database |
| koname | Takes ko id as input and returns ko details |
| taxnam.sql | Takes NCBI taxonomy id as input and returns ko details |
| contractMetab | Simplifies KEGG metabolic graph |
| igraph2gexf | Encodes Igraph into gexf format |
| sigmaGraph | Generates an interactive graph representation of a subnetwork in html using the htmlwidgets package |
| grepgraph | given a set of KOs get the subgrap of metabolism |
| grepgraph.cpd | given a set of CPDs get the subgrap of metabolism |
| annotateContigs.taxonomy | |
| buildE | |
| buildTree | |
| extractFromPath | |
| findK | |
| findSeeds | |
| findTrios | |
| findtype | |
| getContigs | |
| gi2rank | |
| ig2ggvis | |
| ksCal | |
| lca | |
| make.data.frame | Utily function dbquery might return data.frame where each column is a nested list. Converts lilst to dataframe |
| trio | |
| trio.local |