R package for querying integrated -omics database.
.
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 (Unpublished)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
- Annotation DIAMOND - Labelling (round2) more for taxonomic annotation
- MEGAN6 CE - Taxonomic binning of contigs based on labels
- 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)
- the contigs
- just the MDR Region
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
biocondamay depend on packages fromconda-forge.
conda install -c bioconda -c conda-forge bioconductor-shortread
Graph based database combining KEGG + Taxnoomy + Sequencing data (contig) .
R package for mapping reads onto contigs/MDR using Blat
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 |