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README.md

Viral Voyager

TaraCyc contains the first ever large-scale mapping of viral metabolomics data collected from ocean environments around the world. The Tara Oceans Project travelled worldwide collecting water samples for shotgun metagenomic sequencing. This genomic data has been mapped to metabolomic pathways. Recently, viruses have been shown to encode proteins that interact with host metabolic pathways in ways not previously explored, such as a set of cyanophage that modified photosynthetic activity in infected cyanobacteria in order to promote viral replication (Thompson et al).

The TaraCyc website contains all of this analysed metaviriome data with an interactive, user-friendly interface. The website can be accessed at: Tara Viral Voyager.

Website Use

The Map page contains an interactive map with filtering options to visulaize the distribution of viral samples and the data associated with them. Filtered dataset can also be saved for analysis. The Analysis page allows options for analysing the the groups generated on the map page. Users can generate heatmaps, BLANK.

Source Code Information

Software Requirements:

R

Packages

  • dplyr
  • readr
  • shiny
  • leaflet
  • DT
  • magrittr
  • httr
  • jsonlite
  • shinydashboard
  • glue
  • mapedit
  • sf
  • reshape2
  • tibble
  • pheatmap
  • shinythemes

Installation Instructions:

  1. Clone the git repository to local environment
  2. Open the project in R Studio
  3. Open the InstallDependencies.R script and run with "Source on Save" selected
  4. Open the server.R script and select "Run App"

Data Explanation

Parameters To Filter With

  • Sample: Sample IDs begin with c (bacterial fraction), ERR (viral fraction), or F (combined fractions)
  • Sample Type: SINGLE (only one sample), MULTI (multiple samples analysed together), GOV (single viral sample), GOV-MULTI (multiple viral samples)
  • Depth (categorical values that describe the functional depth - metres below surface vary by environment):
    • DCM - deep chlorophyll maximum
    • SRF - surface water layer
    • MES - mesopelagic
    • Mix -
    • MULTI -
  • Depthm - the depth in meters below the surface
  • Pathway Level 1-3: Categories of metabolic activity at varying levels of granularity. Level 1 is the most broad and Level 3 is the most specific
  • Pathway Common Name: Single metabolic pathway
  • Geo Region: Broad geographic region from which 1+ samples were collected
  • RPKM - Reads per kilobase of transcript per million mapped reads (essentially, a normalized genomic abundance measure for genes involved in a given pathway)