9. Third Party Tools

9.2. Annotation

Warning

tbl2asn must be compiled within the past year to function. We attempt to recompile every 6 months or so. Most recent compilation is 27 Feb 2018

9.3. Alignment

9.4. Taxonomy Classification

9.5. Phylogeny

9.6. Specialty Genes

9.7. Visualization and Graphic User Interface

9.8. Utility

  • BEDTools

  • R

  • R_Packages

    • Custom built direcotry containing all the packages required to install R packages offline
    • The majority of the packages were downloaded automatically using the following R commands.

    # Function to get dependencies and imports for a given list of packages.

    getPackages <- function(packs){
            packages <- unlist(
            tools::package_dependencies(packs, available.packages(), which=c("Depends", "Imports"), recursive=TRUE)
            )
    packages <- union(packs, packages)
    packages
    }
    

    # Use the function by providing the names of the desired packages.

    packages <- getPackages(c("packageName", "packageName2"))
    # For example
    #packages <- getPackages(c("MetaComp","gtable","gridExtra","devtools","phyloseq","webshot","plotly","shiny","DT","ape", "igraph", "vegan","BH","plogr","dplyr","ade4","iterators"))
    

    # Download packages to current/desired directory.

    download.packages(packages, destdir="./", type="source")
    
    • The packages specific to bioconductor (‘phyloseq’, ‘Biobase’, ‘biomformat’, ‘rhdf5’, ‘BiocGenerics’, ‘Biostrings’, ‘multtest’) needed to be manually downloade from the site.

    • stringi defaults to downloading icudt55I.zip from online, the following method, from their documentation, was used to build a custom stringi package to avoid connecting to the internet.:

      1. File the `git clone https://github.com/gagolews/stringi.git` command.
      2. Edit the `.Rbuildignore` file and get rid of the `^src/icu55/data` line.
      3. Run `R CMD build stringi_dir_name`.
      

    # index the downloaded packages into PACKAGES files.

    require(tools)
    write_PACKAGES('.')
    
  • MetaComp: EDGE Taxonomy Assignments Visualization

  • GNU_parallel

    • Citation: O. Tange (2011): GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47
    • Site: http://www.gnu.org/software/parallel/
    • Version: 20140622
    • License: GPLv3
  • tabix

  • Primer3

  • SAMtools

9.9. Amplicon Analysis

9.10. RNA-Seq Analysis