: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications.
: Learning regulatory programs by threshold SVD regression.
: Isoform Detection and Prediction.
: Computationally efficient multivariate density estimation package.
: Improving PacBio Long Read Accuracy by Short Read Alignment.
: Fast and Accurate Read Alignment for Resequencing.
: Splice Junction Discovery Using RNA-Seq.
: RNA-Seq Analyzer.
: Junction and Exon array Toolkit for Transcriptome Analysis.
: An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
: A compact stand-alone Genome Browser.
: A tool for mapping millions of short sequences to the genome.
: Combining scientific and statistical significance in gen ranking in Microarray analysis.
: a tool for discovery of differential alternative splicing by exon array.
(has been incorporated to
): Gene-level Background Adjusted Selected probe Expression. A freely available tool for computing Affymetrix Exon array gene-level expression estimates.
: de novo discovery of cis-regulatory modules in multiple species.
: a SVM-based method for doing supervised pattern recognition (classification) with microarray gene expression data .
: a tool designed for tiling array data analysis.
: Scan for cis-regulatory modules with given motif weight matrices.
DNA-Chip Analyzer (dChip)
: Low-level and high-level analysis of oligonucleotide microarrays
: Graphical data mining tool for microarray data using Gene Ontology information
: Scalable communication, combination, and coordination among various types of biology databases
: Gene-centric biological information management tool for post-experiment research
SAGE Data Analysis
: SAGE data analysis tool.
: De novo discovery of cis-regulatory modules
: Extracting gene annotation and Gene Ontology information for microarray analysis
: A resampling based clustering method for microarray data
cDNA Microarray Analysis
: Quality filtering, channel normalization, models of variations and assessment of gene effects
Gifi Array Analyzer
: Analyzing microarray data with Homogeneity Analysis
, Bio-X program, Stanford University | James Clark Center, 318 Campus Drive, Stanford, CA 94305-4065