MetamapsDB

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R package for querying integrated -omics database.

Introduction

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

  1. Gene centric queries
  2. 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 (Unpublished)

  1. Annotation DIAMOND - Labelling of short reads using, blastX-like against NR protein database (more for functional)
  2. Binning MEGAN6 CE - Functional (KEGG) binning of NGS short reads based on labels
  3. Bin-based Assembly NEWBLER - Gene Centric OLC Assembly of functional bins / KEGG Orthologs
  4. Gene centric analyses pAss -
  5. mapBlat - Maps (using BLAT) gDNA and rRNA short onto

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

mapBlat

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