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 (Unpublished)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
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 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
||
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