Description: Launches a 'shiny' based application for Nuclear Magnetic Resonance (NMR)data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of STOCSY method could be found at Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>.
Depends: R(>= 3.6), shinyBS(>= 0.61), shinyWidgets(>= 0.4.3)

Title: image-based High-Throughput RNAi Screening Analysis Tool
Description: image-based high-throughput RNAi screening tools for data analysis

Description: Multi-data type subtyping, which is data type agnostic and accepts missing data. Subtyping is performed using intermediary assessments created with autoencoders and similarity calculations.
Imports: ConsensusClusterPlus, cluster (>= 1.14.4), keras, tensorflow,

Package: iSubpathwayMiner
Version: 1.0
Title: The package can implement the graph-based reconstruction,
analyses, and visualization of the KEGG pathways.
Author: Chunquan Li
Maintainer: Chunquan Li <lcqbio@yahoo.com.cn>
Description: The package can implement the graph-based reconstruction,
analyses, and visualization of the KEGG pathways. (1) Our
system provides many strategies of converting pathways to graph
models. Ten functions related to conversion from pathways to
graphs are developed. Furthermore, the combinations of these
functions can get many combined conversion strategies of
pathway graphs (> 20). (2) The iSubpathwayMiner can support the
annotation and identification of pathways based on gene sets,
compound sets, and even the combined sets of genes and
compounds. The entire pathway and subpathway identification
methods are available for these sets. (3) The system can also
support topology-based pathway analysis of these sets. (4) We
develop KEGG layout style of pathway graphs in R to simulate
the layout of the pathway picture in KEGG website. In addition,
our system has also provided many types of automatic layout
styles. Pathway graphs can also be exported to the GML format
supported by Cytoscape. (5) The iSubpathwayMiner can provide
the most up-to-date pathway analysis results for users.
Multiple species (about 139 Eukaryotes, 1141 Bacteria and 93
Archaea) and different gene identifiers (KEGG compound, Entrez
Gene IDs, gene official symbol, NCBI-gi IDs, UniProt IDs, PDB
IDs, etc.) can also be supported by the system.
Depends: R (>= 2.10.0),graph(>= 1.24.0),RBGL(>= 1.24.0),igraph(>=
0.5.2),XML(>= 3.1-0),fdrtool(>= 1.2.4),utils
Collate: initialize.R visualize.R go2go.R pathway.R metabolic.R
non-metabolic.R metabolic_non-metabolic.R annotation.R
subpathway-method.R topologicalanalysis.R combindedNetwork.R
sample.R
License: GPL (>= 2)
biocViews: Statistics, Annotation, Pathways, Graphs, Networks
Packaged: 2012-01-06 12:28:28 UTC; ripley
Repository: CRAN
Date/Publication: 2012-01-06 12:29:46