Package: FourCSeq
Type: Package
Title: Package analyse 4C sequencing data
Version: 1.4.0
Date: 2015-06-16
Author: Felix A. Klein, EMBL Heidelberg
Maintainer: Felix A. Klein <felix.klein@embl.de>
Depends: R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11),
        splines, methods, LSD
Imports: DESeq2, Biobase, Biostrings, GenomicRanges,
        SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer,
        fda, GenomicAlignments, gtools, Matrix
Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene
VignetteBuilder: knitr
Description: FourCSeq is an R package dedicated to the analysis of
    (multiplexed) 4C sequencing data. The package provides a
    pipeline to detect specific interactions between DNA elements
    and identify differential interactions between conditions. The
    statistical analysis in R starts with individual bam files for
    each sample as inputs. To obtain these files, the package
    contains a python script (extdata/python/demultiplex.py) to
    demultiplex libraries and trim off primer sequences. With a
    standard alignment software the required bam files can be then
    be generated.
License: GPL (>= 3)
biocViews: Software, Preprocessing, Sequencing
Built: R 3.3.2; ; 2017-06-15 11:32:48 UTC; unix
