Package: HiCBricks
Title: Framework for Storing and Accessing Hi-C Data Through HDF Files
Version: 1.2.0
Description: A flexible framework for storing and accessing high-resolution Hi-C data through HDF files. HiCBricks allows import of Hi-C data through various formats such as the 2D matrix format or a generalized n-column table formats. In terms of access, HiCBricks offers functions to retrieve values from genomic loci separated by a certain distance, or the ability to fetch matrix subsets using word alike terms. HiCBricks will at a later point offer the ability to fetch multiple matrix subsets using fewer calls. It offers the capacity to store GenomicRanges that may be associated to a particular Hi-C experiment, to do basic ranges overlap (any, within) with the Hi-C experiment associated Ranges object and also to store any metadata that users may think to be relevant for their Hi-C experiment. Finally, you can do TAD calls with LSD and create pretty heatmaps.
Date: 2019-02-03
Type: Package
Authors@R: c(
    person("Koustav", "Pal", ,"koustav.pal@ifom.eu", c("aut", "cre")),
    person("Carmen", "Livi", ,"carmen.livi@ifom.eu", c("ctb")),
    person("Ilario", "Tagliaferri", ,"ilario.tagliaferri@ifom.eu", c("ctb")))
Maintainer: Koustav Pal <koustav.pal@ifom.eu>
License: MIT + file LICENSE
Depends: R (>= 3.5), utils, curl, rhdf5, R6, grid
Imports: ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
        data.table, GenomeInfoDb, GenomicRanges, stats, IRanges,
        grDevices, S4Vectors, digest
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
biocViews: DataImport, Infrastructure, Software, Technology,
        Sequencing, HiC
git_url: https://git.bioconductor.org/packages/HiCBricks
git_branch: RELEASE_3_9
git_last_commit: e2a588c
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
NeedsCompilation: no
Packaged: 2019-05-03 03:17:24 UTC; biocbuild
Author: Koustav Pal [aut, cre],
  Carmen Livi [ctb],
  Ilario Tagliaferri [ctb]
Built: R 3.6.1; ; 2019-07-27 21:45:04 UTC; unix
