ACANA ACANA is an accurate and consistent alignment tool for DNA sequences.
Analysis of Genetic Associations for Shared Controls Design ("/Rhythmyx/assembler/render?sys_contentid=35154&sys_revision=8&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35154" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35154" sys_siteid="" sys_folderid="")P-value based analysis for shared controls design in genome-wide association studies.
ART("/Rhythmyx/assembler/render?sys_contentid=34834&sys_revision=9&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34834" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34834" sys_siteid="" sys_folderid="") ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data.
Case Control ("/Rhythmyx/assembler/render?sys_contentid=56407&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56407" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56407" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for a design that includes two samples from the same population: one sample of affected individuals and their mothers and a second sample of unaffected individuals and their mothers.
Circular FSA ("/Rhythmyx/assembler/render?sys_contentid=51492&sys_revision=2&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="51492" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="51492" sys_siteid="" sys_folderid="")A SAS extention that tests whether the orthologs {B1,B2,...,BG} satisfy the same relative order as the genes { A1,A2,...,AG }.
coMotif("/Rhythmyx/assembler/render?sys_contentid=34836&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34836" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34836" sys_siteid="" sys_folderid="") A three-component mixture framework to model the joint distribution of two motifs as well as the situation where some sequences contain only one or none of the motifs.
Correlation-Based Tests ("/Rhythmyx/assembler/render?sys_contentid=35146&sys_revision=5&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35146" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35146" sys_siteid="" sys_folderid="")Correlation-based inference for linkage disequilibrium with multiple alleles.
Ctrl-mom-hybrid ("/Rhythmyx/assembler/render?sys_contentid=56408&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56408" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56408" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for a hybrid design that includes a sample of affected individuals and their parents and a sample of unaffected individuals and their mothers (case-parent triad/control-mother dyad design).
EagleView EagleView is an information-rich viewer for next-generation genome assembles with data integration capability.
EpiCenter ("/Rhythmyx/assembler/render?sys_contentid=34838&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34838" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34838" sys_siteid="" sys_folderid="")EpiCenter is a powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications.
Expression Predictor (ExP) ("/Rhythmyx/assembler/render?sys_contentid=34881&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34881" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34881" sys_siteid="" sys_folderid="")A desktop application developed with Java programming language for classifying and predicting samples based on gene expression data using a simplified fuzzy adaptive resonance theory map (SFAM) neural network architecture.
Extracting Patterns and Identifying co-expressed Genes (EPIG) ("/Rhythmyx/assembler/render?sys_contentid=34840&sys_revision=5&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34840" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34840" sys_siteid="" sys_folderid="")A method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes.
fdrMotif ("/Rhythmyx/assembler/render?sys_contentid=34887&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34887" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34887" sys_siteid="" sys_folderid="")Determines the number of binding sites in each sequence of a probability model by performing statistical tests.
GA/KNN ("/Rhythmyx/assembler/render?sys_contentid=34892&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34892" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34892" sys_siteid="" sys_folderid="")Selects the most discriminative variables for sample classification and may be used for analysis of microarray gene expression data, proteomic data or other high-dimensional data.
GADEM("/Rhythmyx/assembler/render?sys_contentid=34890&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34890" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34890" sys_siteid="" sys_folderid="") An unbiased de novo motif discovery tool implementing an expectation-maximization (EM) algorithm.
GEI-TRIMM ("/Rhythmyx/assembler/render?sys_contentid=56417&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56417" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56417" sys_siteid="" sys_folderid="")This package includes the program GEI-TRIMM, which implements the method described in the manuscript Shi M, Umbach DM, Weinberg CR 2010 "Testing Haplotype-Environment Interactions Using Case-parent Triads."
Genetic Algorithm Method for Optimizing a Position Weight Matrix ("/Rhythmyx/assembler/render?sys_contentid=34945&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34945" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34945" sys_siteid="" sys_folderid="")Implements a simple method to improve a poorly estimated position weight matrix using chromatin immunoprecipitation data.
Hill Viewer ("/Rhythmyx/assembler/render?sys_contentid=34951&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34951" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34951" sys_siteid="" sys_folderid="")Used to visualize dose-response curves and relative potency functions based on two sets of Hill model parameters.
Hybrid Design ("/Rhythmyx/assembler/render?sys_contentid=34981&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34981" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34981" sys_siteid="" sys_folderid="")Provides information for fitting log-linear models and carrying out statistical tests.
LEM scripts ("/Rhythmyx/assembler/render?sys_contentid=56421&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56421" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56421" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for preterm birth study.
Modk-Prototypes ("/Rhythmyx/assembler/render?sys_contentid=35062&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35062" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35062" sys_siteid="" sys_folderid="")Clusters biological samples by simultaneously considering microarray gene expression data and classes of known phenotypic variables such as clinical chemistry evaluations and histopathologic observations.
OMiMa The OMiMa System is a computational tool for identifying functional motifs in DNA or protein sequences.
ORIOGEN v 3 - Order Restricted Inference for Ordered Gene Expression ("/Rhythmyx/assembler/render?sys_contentid=35065&sys_revision=8&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35065" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35065" sys_siteid="" sys_folderid="")Analyzes gene expression data obtained from time-course/dose-response studies.
PCA-based Gene Filtering ("/Rhythmyx/assembler/render?sys_contentid=35076&sys_revision=2&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35076" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35076" sys_siteid="" sys_folderid="")A new filtering statistic for Affymetrix GeneChips, based on principle component analysis (PCA) on the probe-level gene expression data.
Phase-shifted Analysis of Gene Expression (PAGE) ("/Rhythmyx/assembler/render?sys_contentid=35110&sys_revision=2&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35110" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35110" sys_siteid="" sys_folderid="")An interactive tool that uses a line graph to dynamically illustrate the phase-shifted patterns of gene expressions based on the q-Cluster selected by the users.
Principal Variance Component Analysis("/Rhythmyx/assembler/render?sys_contentid=35299&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35299" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35299" sys_siteid="" sys_folderid="") A hybrid approach using principal components analysis and variance component analysis as a methodology to determine and quantify sources of variability most prominent in microarray gene expression data.
PSPE PSPE is a computational tool specifically designed for simulating evolution of non-coding DNA sequences, in particular promoter sequences.
R code for fitting Random Periods Model("/Rhythmyx/assembler/render?sys_contentid=51500&sys_revision=2&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="51500" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="51500" sys_siteid="" sys_folderid="") Software for fitting the Random Periods Model (RPM) for cell cycle genes.
Rankings of causal loci in GWAS ("/Rhythmyx/assembler/render?sys_contentid=35144&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35144" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35144" sys_siteid="" sys_folderid="")Novel rank-based approaches for discovery and replication in genome wide association studies.
R-SCRIPTS ("/Rhythmyx/assembler/render?sys_contentid=56430&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56430" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56430" sys_siteid="" sys_folderid="")This package contains two R scripts for generating scenarios 1-4 described in the manuscript Shi M, Weinberg CR 2011 "How much are we missing in SNP-by-SNP analyses of GWAS?"
SA-Modk-Prototypes ("/Rhythmyx/assembler/render?sys_contentid=35617&sys_revision=2&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35617" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35617" sys_siteid="" sys_folderid="")For simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations using simulated annealing.
SAS Code to Fit Genetic Models ("/Rhythmyx/assembler/render?sys_contentid=56439&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56439" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56439" sys_siteid="" sys_folderid="")Various SAS code for identifying genes related to a quantitative trait, incorporating multiple siblings and missing parents.
TRIad Multi-Marker ("/Rhythmyx/assembler/render?sys_contentid=35906&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35906" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35906" sys_siteid="" sys_folderid="")Performs association tests for a child's or mother's genetic effects using multiple markers from triad families.
TRIMMEST ("/Rhythmyx/assembler/render?sys_contentid=56435&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56435" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56435" sys_siteid="" sys_folderid="")This package contains programs that fit log-linear models to estimate the relative risk associated with a candidate risk haplotype in a triad-based association study.
mPopTag ("/Rhythmyx/assembler/render?sys_contentid=35063&sys_revision=6&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35063" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35063" sys_siteid="" sys_folderid="")A tool used to select or evaluate linkage disequilibrium tag SNPs for multiple populations.
TAGster("/Rhythmyx/assembler/render?sys_contentid=35267&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35267" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35267" sys_siteid="" sys_folderid="") A tool to select, evaluate and visualize LD tag SNPs for single or multiple populations.
Forest Plot Viewer program Creates figures using a forest plot display with multiple columns of descriptive text and has the ability to be rapidly modified by the user to display subsets of data based on user-specified filtering criteria.
NMR NOE Simulations ("/Rhythmyx/assembler/render?sys_contentid=35069&sys_revision=2&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35069" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35069" sys_siteid="" sys_folderid="")Calculates the time dependence of the diagonal and crosspeaks in a 2D NOESY experiment for a system undergoing chemical exchange using the full relaxation matrix.
NvAssign ("/Rhythmyx/assembler/render?sys_contentid=34773&sys_revision=5&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34773" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34773" sys_siteid="" sys_folderid="")Software that aids the process of protein resonance in NMR.
Electron Spin Resonance Software Database ("/Rhythmyx/assembler/render?sys_contentid=34873&sys_revision=3&sys_variantid=787&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="787" sys_dependentid="34873" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34873" sys_siteid="" sys_folderid="")A compilation of details about programs written for Electron Paramagnetic Resonance spectroscopists.
Public Electron Paramagnetic Resonance Software Tools ("/Rhythmyx/assembler/render?sys_contentid=32797&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="32797" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="32797" sys_siteid="" sys_folderid="")Helps researchers analyze Electron Paramagnetic Resonance data.
