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Genetic Analysis: GWAS Genetic Variation Linkage Analysis Gene Expression
Sequence Analysis: Assembly Annotation Alignment RNAi RNA-seq Primer Design Next Generation Tools Phylogenetic Analysis Gene Structure Viral
AmosCmp16Spipeline uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene.
CellProfiler cell image analysis software quantitatively measures phenotypes from thousands of images automatically, usually for high-throughput image-based cell screening experiments.
CellProfiler Analyst data exploration and analysis software is designed for complex and interactive exploration of multidimensional data, specifically from high-throughput image-based experiments.
ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
GenePattern is a powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research..
The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable the rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of efficiently accessing the next-generation sequencing data, researchers and developers are free to focus on their specific analysis algorithms. This not only vastly improves the productivity of developers, who can quickly write new analyses, but also results in tools that are efficient and robust, and can benefit from improvements to a common data management engine.
Haploview is designed to facilitate the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.