MetamapsDB

R package for querying integrated -omics database.

Introduction

MetamapsDB is a R package used for interfacing with such a database for

^ 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 (Unpublished)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
mapBlat - Maps (using BLAT) gDNA and rRNA short onto
- the contigs
- just the MDR Region

Docker wrapper for generating a KEGG + Taxnoomy + Contig neo4j graph database

R package for mapping reads onto contigs/MDR using Blat

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