Exploratory analysis for two-color spotted microarray data

Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions
        from Agnes Paquet and Sandrine Dudoit.

Yee Hwa (Jean) Yang <jean@biostat.ucsf.edu>

Class definitions for two-color spotted microarray data.
        Fuctions for data input, diagnostic plots, normalization and
        quality checking.

maClasses.R maGet.R maSet.R maPrint.R maSubset.R maBind.R
maComp.R maDots.R maInput.R maNorm.R maOutput.R maWidget.R
maPlots.R maAnnotate.R maRankGenes.R maSMA.R maSearch.R
maWrap.R

Platform for integrative analysis of omics data

c(person("Leif", "Varemo Wigge", email =
"piano.rpkg@gmail.com", role = "aut"), person("Intawat",
"Nookaew", email = "piano.rpkg@gmail.com", role = "aut"))

Leif Varemo Wigge <piano.rpkg@gmail.com> and Intawat Nookaew <piano.rpkg@gmail.com>

BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods

yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle

Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.

Microarray, Preprocessing, QualityControl,
DifferentialExpression, Visualization, GeneExpression,
GeneSetEnrichment, Pathways

Dirk Eddelbuettel <edd@debian.org> with contributions 
 by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
 Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
 Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, 
 Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell,
 Matthew de Queljoe, Ion Suruceanu, and Bill Denney.

Create Compact Hash Digests of R Objects

Implementation of a function 'digest()' for the creation 
 of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 
 'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy
 comparison of R language objects, as well as functions such as'hmac()' to
 create hash-based message authentication code. Please note that this package
 is not meant to be deployed for cryptographic purposes for which more
 comprehensive (and widely tested) libraries such as 'OpenSSL' should be
 used.