Package: DGCA
Title: Differential Gene Correlation Analysis
Description: Performs differential correlation analysis on input
matrices, with multiple conditions specified by a design matrix. Contains
functions to filter, process, save, visualize, and interpret differential
correlations of identifier-pairs across the entire identifier space, or with
respect to a particular set of identifiers (e.g., one). Also contains several
functions to perform differential correlation analysis on clusters (i.e., modules)
or genes. Finally, it contains functions to generate empirical p-values for the
hypothesis tests and adjust them for multiple comparisons. Although the package
was built with gene expression data in mind, it is applicable to other types of
genomics data as well, in addition to being potentially applicable to data from
other fields entirely. It is described more fully in the manuscript
introducing it, freely available at <doi:10.1186/s12918-016-0349-1>.
Version: 1.0.2
Author: Bin Zhang [aut],
Andrew McKenzie [aut, cre]
Maintainer: Andrew McKenzie <amckenz@gmail.com>
Depends: R (>= 3.2)
Imports: WGCNA, matrixStats, methods
Suggests: knitr, impute, gplots, fdrtool, testthat, ggplot2, plotrix,
GOstats, HGNChelper, org.Hs.eg.db, AnnotationDbi, abind,
MEGENA, Matrix, doMC, igraph, cowplot, stats, utils
VignetteBuilder: knitr
RoxygenNote: 5.0.1
License: GPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2019-12-09 02:23:17 UTC; mckena01
Repository: CRAN
Date/Publication: 2019-12-09 10:30:16 UTC

Package: DGEobj
Type: Package
Title: Differential Gene Expression (DGE) Analysis Results Data Object
Version: 1.0.1
Description:
Provides a flexible container to manage and annotate Differential Gene
Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>).
The DGEobj has data slots for row (gene), col (samples), assays (matrix n-rows
by m-samples dimensions) and metadata (not keyed to row, col, or assays).
A set of accessory functions to deposit, query and retrieve subsets of a data
workflow has been provided.  Attributes are used to capture metadata such as
species and gene model, including reproducibility information such that a 3rd
party can access a DGEobj history to see how each data object was created or
modified.  Since the DGEobj is customizable and extensible it is not limited
to RNA-seq analysis types of workflows -- it can accommodate nearly any data
analysis workflow that starts from a matrix of assays (rows) by samples (columns).
Authors@R:
c(person("John", "Thompson", role = "aut", email = "jrt@thompsonclan.org"),
person("Connie", "Brett",  role = c("aut", "cre"), email = "connie@aggregate-genius.com"),
person("Isaac", "Neuhaus", role = "aut", email = "isaac.neuhaus@bms.com"),
person("Ryan", "Thompson", role = "aut", email = "rct@thompsonclan.org"))
Depends: R (>= 3.5.0)
License: GPL-3
Language: en-US
Encoding: UTF-8
Imports: assertthat, magrittr, stringr, utils, GenomicRanges
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat, edgeR
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-12-03 19:18:21 UTC; conniebrett
Author: John Thompson [aut],
Connie Brett [aut, cre],
Isaac Neuhaus [aut],
Ryan Thompson [aut]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Repository: CRAN
Date/Publication: 2020-12-07 09:30:02 UTC