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Last data update: 2014.03.03

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diffHic : Differential Analyis of Hi-C Data

Package: diffHic
Version: 1.4.2
Date: 2016-06-14
Title: Differential Analyis of Hi-C Data
Author: Aaron Lun <alun@wehi.edu.au>
Maintainer: Aaron Lun <alun@wehi.edu.au>
Depends: R (>= 3.3.0), GenomicRanges, InteractionSet,
SummarizedExperiment
Imports: Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma,
csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb,
BiocGenerics, grDevices, graphics, stats, utils
Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix
biocViews: MultipleComparison, Preprocessing, Sequencing, Coverage,
Alignment, Normalization, Clustering, HiC
Description: Detects differential interactions across biological
conditions in a Hi-C experiment. Methods are provided for read
alignment and data pre-processing into interaction counts.
Statistical analysis is based on edgeR and supports
normalization and filtering. Several visualization options are
also available.
License: GPL-3
NeedsCompilation: yes
LinkingTo: Rhtslib, zlibbioc
Packaged: 2016-06-15 05:18:26 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing
● 15 images, 34 functions, 0 datasets
● Reverse Depends: 0

GenomicInteractions : R package for handling genomic interaction data URL: https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/

Package: GenomicInteractions
Type: Package
Title: R package for handling genomic interaction data
URL:
https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
Version: 1.6.2
Date: 2015-07-20
Author: Harmston, N., Ing-Simmons, E., Perry, M., Baresic, A., Lenhard,
B.
Maintainer: Malcolm Perry <mgperry32@gmail.com>,
Liz Ing-Simmons <liz.ing-simmons12@csc.mrc.ac.uk>
Imports: Rsamtools, rtracklayer, GenomicRanges, IRanges, BiocGenerics
(>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid,
gridExtra, methods, igraph, S4Vectors, dplyr, Gviz, Biobase,
graphics, stats, utils
Suggests: knitr, BiocStyle, testthat
VignetteBuilder: knitr
Description: R package for handling Genomic interaction data, such as
ChIA-PET/Hi-C, annotating genomic features with interaction
information and producing various plots / statistics.
biocViews: Software,Infrastructure,DataImport,DataRepresentation,HiC
License: GPL-3
Depends: R (>= 3.3), InteractionSet
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 04:53:42 UTC; biocbuild

● Data Source: BioConductor
● BiocViews: DataImport, DataRepresentation, HiC, Infrastructure, Software
● 9 images, 39 functions, 4 datasets
● Reverse Depends: 0