DESCRIPTION

Package: slimR
Type: Package
Title: Short Linear Motif (SLiM) Analysis in the context of human diseases
Version: 0.99.3
Date: 2018-11-08
Authors@R: c(person("Bora", "Uyar", email='bora.uyar@mdc-berlin.de', role=c("aut", "cre")))
Description: slimR is a protein sequence analysis package centered around 
  short linear motifs (SLiMs) and their connections to human diseases.  
  The package contains functions to retrieve data from public databases 
  such as ELM (elm.eu.org), UniProt (uniprot.org). Annotated SLiMs and 
  SLiM patterns  (regular expressions) are retrieved from the ELM database. 
  Protein sequence  features such as disease-causing mutations, polymorphisms, 
  protein domains,  and many other annotated features are retrieved from the 
  UniProt or ClinVar databases.  The main motivation of the package is to facilitate 
  analysis of the impact of protein sequence variations due to mutations 
  and polymorphism on the content of SLiMs. Besides functions to retrieve 
  data from public resources, there are functions to calculate disorder 
  scores, search for SLiM instances in given sequences, look for gain/loss 
  of SLiMs due to sequence variations. The package should be useful not 
  only for the analysis of human diseases but also studies of the evolution 
  of species via gain/loss of SLiMs in any comparative context.
Depends: R (>= 3.5.0)
Imports: GenomicRanges,
    data.table,
    dplyr,
    pbapply,
    RCurl,
    XML,
    stringr,
    pracma,
    Biostrings,
    parallel,
    S4Vectors, 
    R.utils
License: Artistic-2.0
LazyData: TRUE
RoxygenNote: 6.1.0
Suggests: testthat