Package: LncMod
Type: Package
Title: Predicting Modulator and Functional/Survival Analysis
Version: 1.1
Author: Yongsheng Li,Zishan Wang,Juan Xu*,Xia Li*
Maintainer: Zishan Wang <azureskyeric@gmail.com>
Description: Predict modulators regulating the ability of effectors to regulate their targets and produce
modulator-effector-target triplets followed by goterm functional enrichment and survival analysis.This
is mainly applied to long non-coding RNAs (lncRNAs) as candidate modulators regulating the ability of
transcription factors (TFs) to regulate their corresponding targets.
License: GPL-2
LazyData: TRUE
biocViews: long non-coding
RNA,lncRNA,modulator,triplet,function,survival
Depends: R (>= 2.15.2), survival, pheatmap, parallel
Packaged: 2015-06-27 00:29:50 UTC; Administrator
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-06-27 13:24:19
Package: MM2S
Type: Package
Version: 1.0.5
Date: 2015-02-24
Title: Single-Sample Classifier of Medulloblastoma Subtypes for
Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Description: Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.
Author: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Maintainer: Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
Depends: GSVA (>= 1.13.1), kknn (>= 1.2-5), parallel, lattice, pheatmap, R (>= 2.10)
Suggests: knitr, MM2Sdata
Imports: datasets, grDevices, graphics, stats, utils
VignetteBuilder: knitr
License: GPL-3
biocViews: MM2Sdata, Cancer, Classification, Microarray, Software,
Visualization
URL:
http://www.sciencedirect.com/science/article/pii/S0888754315000774,
http://www.pmgenomics.ca/bhklab/software/mm2s
LazyData: yes
NeedsCompilation: no
Packaged: 2016-02-24 23:10:44 UTC; DeenaGendoo
Repository: CRAN
Date/Publication: 2016-02-25 00:39:19
Package: KOGMWU
Type: Package
Title: Functional Summary and Meta-Analysis of Gene Expression Data
Version: 1.0
Date: 2015-03-02
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Description: Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
License: GPL-3
Depends: R (>= 2.10), pheatmap
Packaged: 2015-03-05 07:12:15 UTC; c-monster
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-03-05 08:49:58
providing 
.