Package: maPredictDSC
Version: 1.10.0
Date: 2013-6-27
Title: Phenotype prediction using microarray data: approach of the best
overall team in the IMPROVER Diagnostic Signature Challenge
Author: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Depends: R (>= 2.15.0), MASS, affy, limma, gcrma, ROC, class, e1071, caret, hgu133plus2.db, ROCR, AnnotationDbi, LungCancerACvsSCCGEO
Suggests: parallel
Maintainer: Adi Laurentiu Tarca <atarca@med.wayne.edu>
Description: This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.
License: GPL-2
URL: http://bioinformaticsprb.med.wayne.edu/maPredictDSC
biocViews: Microarray, Classification
Collate: aggregateDSC.R perfDSC.R predictDSC.R maPredictDSC.R
Imports:
LazyLoad: yes
Packaged: 2016-05-04 05:01:21 UTC; biocbuild
NeedsCompilation: no
Package: TCC
Type: Package
Title: TCC: Differential expression analysis for tag count data with
robust normalization strategies
Version: 1.12.1
Author: Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji
Kadota
Maintainer: Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki
Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
Description: This package provides a series of functions for performing
differential expression analysis from RNA-seq count data using
robust normalization strategy (called DEGES). The basic idea of
DEGES is that potential differentially expressed genes or
transcripts (DEGs) among compared samples should be removed
before data normalization to obtain a well-ranked gene list
where true DEGs are top-ranked and non-DEGs are bottom ranked.
This can be done by performing a multi-step normalization
strategy (called DEGES for DEG elimination strategy). A major
characteristic of TCC is to provide the robust normalization
methods for several kinds of count data (two-group with or
without replicates, multi-group/multi-factor, and so on) by
virtue of the use of combinations of functions in depended
packages.
Depends: R (>= 2.15), methods, DESeq, DESeq2, edgeR, baySeq, ROC
Imports: samr
Suggests: RUnit, BiocGenerics
Enhances: snow
License: GPL-2
Copyright: Authors listed above
biocViews: Sequencing, DifferentialExpression, RNASeq
NeedsCompilation: no
Packaged: 2016-05-27 04:20:14 UTC; biocbuild
providing 
.