README.md

In Snitkin-Lab-Umich/regentrans: A framework and R package for using genomics to study regional pathogen transmission

regentrans: R package for investigating regional pathogen transmission using genomic data

Website: https://snitkin-lab-umich.github.io/regentrans/

Manuscript: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000747

regentrans can be installed using the command devtools::install_github('Snitkin-Lab-Umich/regentrans') in R

Examples of how to interrogate all of the questions in the table below can be found in the introductory vignette.

Questions regentrans can help investigate:

| Question | Method | regentrans function(s) | Required Data | Optional Data |---|---|---|---|---| |How do you choose pairwise SNV distance thresholds?| Fraction of intra-facility pairs for different pairwise SNV distances |get_frac_intra()|output of get_pair_types()| | | Is transmission occurring within and/or between locations? | Phylogenetic clustering of isolates from the same location | get_clusters() | Phylogenetic tree, isolate location information | | | | Pairwise SNV distances within and between facilities | get_pair_types() | A pairwise SNV distance matrix (can be created using ape::dist.dna() on fasta file of variants), isolate location information | | | What locations is transmission occurring within/between? | Population-level similarity between locations via genetic flow (Fsp) | get_genetic_flow() | Fasta file of variants, isolate location information | | | | Number of closely related pairs within and between facilities | Plot code in vignette | | | | Have transmission dynamics changed over time? | Methods above but split over time | | | | | Is transmission occurring along paths of higher patient/person flow? | Compare patient/person flow between locations to inter-location pairwise SNV distances or genetic flow (Fsp) | get_patient_flow()| Patient transfer network edge matrix | | | | Compare patient/person flow between locations to populatoin-level similarity between locations | get_patient_flow(), get_genetic_flow()| Patient transfer network, fasta file of variants, isolate location information | | | Are there any observable geographic trends in prevalence/transmission? | Visualize prevalence and closely related pairs or genetic flow (Fsp) | Plot code in vignette | Geographic locations of each facility, patient transfer network, summary metric of genomic similarity | |

Questions

Please open an issue or contact Evan Snitkin ([e-mail]) with any questions.

Snitkin-Lab-Umich/regentrans documentation built on Jan. 29, 2023, 7:45 a.m.