Tools
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NGS
Transcription Factor Binding
Differential Expression
R Tools
altanalyze - Alternative splicing and functional prediction analysis tool
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types ( Gene 1.0 , Exon 1.0 , junction ) as well as many conventional array-types (e.g., Affymetrix, Illumina, Agilent). This software requires no advanced knowledge of bioinformatics programs or scripting.
Overview Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). From this web site, you can: Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results. Explore the Molecular Signatures Database (MSigDB) , a collection of annotated gene sets for use with GSEA software.
GeneSet Enrichment Analysis
Annotation
Genome Browsers