README.md

In etheleon/metamaps: MetamapsDB: R package for querying Metagenomics data against Metabolic Pathways and Gene Centric Assemblies

MetamapsDB

R package for querying integrated -omics database.

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MetamapsDB is a R package used for interfacing with such a database for Gene centric queries and Analyses of Integrated Genomic and Transcriptomic microbiome data. 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 (Unpublished)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 Gene centric analyses pAss - mapBlat - Maps (using BLAT) gDNA and rRNA short onto

Bin-Based assembly

• Annotation DIAMOND - Labelling (round2) more for taxonomic annotation
• MEGAN6 CE - Taxonomic binning of contigs based on labels

Gene centric Analysis

• 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

• the contigs
• just the MDR Region

Dependencies

R Bioconductor packages

If you're installing this package from from a conda installation of R, it's very likely you'll face some issues with installing ShortRead.

Packages from bioconda may depend on packages from conda-forge.

conda install -c bioconda -c conda-forge bioconductor-shortread

OMICS

Graph based database combining KEGG + Taxnoomy + Sequencing data (contig) .

MapBlat

R package for mapping reads onto contigs/MDR using Blat

mapBlat

Functions

Below is a description of important functions and their uses

| 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 ||

etheleon/metamaps documentation built on May 16, 2019, 9:05 a.m.