person("Nicolas", "Ballarini", email = "nicoballarini@gmail.com",
2.1.1), ggrepel, geoR, grid, gridBase, gridExtra, methods,
plyr, polyclip, scales, shape, sp, survRM2, survival, UpSetR,
Packaged: 2020-01-13 19:40:47 UTC; nicolasballarini

2.1.1), ggrepel, grid, gridBase, gridExtra, methods, plyr,
Packaged: 2020-01-29 02:27:09 UTC; nicolasballarini

Title: Patient Subgroup Identification for Clinical Drug Development
Author: Xin Huang, Yan Sun and Saptarshi Chatterjee
Description: Provides function to apply methods proposed in "Patient Subgroup Identification for Clinical Drug Development"  by Huang et al. (2017) <10.1002/sim.7236>.
Depends: R (>= 2.1.0),AIM, survival, ggplot2, Matrix

Author: Xin Huang, Yan Sun, Saptarshi Chatterjee and Paul Trow
Description: Function Wrapper contains four algorithms for developing threshold-based multivariate (prognostic/predictive) biomarker signatures via bootstrapping and aggregating of thresholds from trees, Monte-Carlo variations of the Adaptive Indexing method and Patient Rule Induction Method. Variable selection is automatically built-in to these algorithms. Final signatures are returned with interaction plots for predictive signatures. Cross-validation performance evaluation and testing dataset results are also output.

Title: Identify Metabolic Subpathways Mediated by MicroRNAs
Description: Routines for identifying metabolic subpathways mediated by microRNAs (miRNAs) through topologically locating miRNAs and genes within reconstructed Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway graphs embedded by miRNAs. (1) This package can obtain the reconstructed KEGG metabolic pathway graphs with genes and miRNAs as nodes, through converting KEGG metabolic pathways to graphs with genes as nodes and compounds as edges, and then integrating miRNA-target interactions verified by low-throughput experiments from four databases (TarBase, miRecords, mirTarBase and miR2Disease) into converted pathway graphs. (2) This package can locate metabolic subpathways mediated by miRNAs by topologically analyzing the "lenient distance" of miRNAs and genes within reconstructed KEGG metabolic pathway graphs.(3) This package can identify significantly enriched miRNA-mediated metabolic subpathways based on located subpathways by hypergenomic test. (4) This package can support six species for metabolic subpathway identification, such as caenorhabditis elegans, drosophila melanogaster, danio rerio, homo sapiens, mus musculus and rattus norvegicus, and user only need to update interested organism-specific environment variables.
Collate: fdr.est.R getBackground.R getEdgeLabel.R getEdgeLty.R
biocViews: Statistics, Annotation, SubPathways, Graphs, MicroRNAs