DESCRIPTION

Package: echotabix
Type: Package
Title: echoverse module: automated creation and querying of tabix files
Version: 0.99.10
Authors@R: 
    c(person(given = "Brian",
           family = "Schilder",
           role = c("cre"),
           email = "brian_schilder@alumni.brown.edu",
           comment = c(ORCID = "0000-0001-5949-2191")),
    person(given = "Jack",
           family = "Humphrey",
           role = c("aut"),
           email = "Jack.Humphrey@mssm.edu",
           comment = c(ORCID = "0000-0002-6274-6620")),
    person(given = "Towfique",
           family = "Raj",
           role = c("aut"),
           email = "towfique.raj@mssm.edu",
           comment = c(ORCID = "0000-0002-9355-5704"))
           ) 
Description: Converts genomic data files to tabix format
    (including liftover, sorting, compression, and indexing steps)
    with a single function. Retrieves local or remote tabix VCF/tabular files
    with helper functions for creating queries from subsets of genomic data 
    (e.g GWAS/QTL loci, genomic ranges). Multiple methods available 
    at each step, including wrapper functions for an up-to-date, 
    `conda`-based installation of `htslib` tools.
URL: https://github.com/RajLabMSSM/echotabix
BugReports: https://github.com/RajLabMSSM/echotabix/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1)
SystemRequirements: Python (>= 3.7.0)
biocViews:
Imports: 
    echodata,
    echoconda,
    utils,
    R.utils,
    tools,
    dplyr,
    methods,
    data.table,   
    GenomeInfoDb, 
    IRanges,
    GenomicRanges,
    Biostrings,
    VariantAnnotation,
    Rsamtools,  
    rtracklayer,
    MungeSumstats (>= 1.3.14),
    BiocManager,
    BiocGenerics
Suggests:
    markdown,
    rmarkdown, 
    knitr,
    BiocStyle,
    covr,
    testthat (>= 3.0.0),
    remotes,
    parallel,
    badger,
    seqminer,
    GenomicFiles
Remotes:
    github::RajLabMSSM/echodata,
    github::RajLabMSSM/echoconda
RoxygenNote: 7.2.3
VignetteBuilder: knitr
License: GPL (>= 3)
Config/testthat/edition: 3