On a standard laptop (i7 chip), the analysis of the example data with default parameters and the WikiPathways annotations takes ∼1 min; analysis with GO annotation takes ∼25 min.
For example, with the default option, Bowtie can map the two million single-end 32 bp reads in 151 s, but 6.4% of confident mappings are wrong.
For example, with the default parameter setting, the PRE, MRR, and AUC are 8.84%, 12.59%, and 88.44% for the tissue-specific PPI with edge removal strategy, respectively, and 7.99%, 13.97%, and 87.03% for the tissue-nonspecific one, respectively.
For example, with the default parameter setting, the PRE, MRR, and AUC are 8.84%, 12.55%, and 88.49% for the node removal strategy, respectively, and 8.84%, 12.59%, and 88.44% for the edge reweight strategy, respectively.
In the next step, the genes in those SNP lists can be used for functional annotation analyses, for example using the Gene Ontology Enrichment Software Toolkit GOEASTT) with default parameters, which will reveal if identified SNP modules are biologically relevant to the trait of interest.
For example, alcoholism and drug abuse have been previously associated with default in new patients [6], [18].
Users can download the example input file for "single" or "multiple" mode and run the tools with default parameters.
For example, in this study, just under 40% of CDC42 could be targeted with default repeat masking settings.
For example, the sucrase-isomaltase (CHEMBL3114) and maltase-glucoamylase (CHEMBL2074) pair share 11 scaffolds with default searching parameters (shared scaffold 5, pChEMBL value 6) (Supplementary Figure S1 ).
For example, the default setting includes all the cloud content along with the music you've placed on the phone manually, which can clutter menus beyond recognition, but it can be easily switched off in the main Music settings).
