• Tools

    Pomelo II

    Pomelo II is a new and much improved incarnation of Pomelo, a tool for finding differentially expressed genes, and genes that are of potential interest because they are related to an outcome of interest (e.g., type of cancer, survival).

    http://bioinformatics.org/asterias/bzr/pomelo2/www/  

     

    Ingenuity Pathway Analysis (IPA)

    Ingenuity Pathways Analysis enables biologists and bioinformaticians to identify the biological mechanisms, pathways, and functions most relevant to their experimental datasets or genes of interest. IPA helps researchers easily search the scientific literature, build dynamic pathway models, quickly analyze experimental data and share research and collaborate.

     http://www.ingenuity.com/products/ipa  

     

    TopHat

    TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the Center for Computational Biology at Johns Hopkins University, the Departments of Mathematics and Molecular and Cell Biology at the University of California, Berkeley and the Department of Stem Cell and Regenerative Biology at Harvard University.

     http://tophat.cbcb.umd.edu/  

     

    GenePattern

    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.

     http://www.broadinstitute.org/cancer/software/genepattern  

     

    The Cancer Genome Atlas (TCGA)

    The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA is a joint effort of the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), two of the 27 Institutes and Centers of the National Institutes of Health, U.S. Department of Health and Human Services.

     http://cancergenome.nih.gov/  

     

    The database of Genotypes and Phenotypes (dbGaP)

    The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype.

     http://www.ncbi.nlm.nih.gov/gap  

     

    TARGET

    TARGET applies a comprehensive genomic approach to determine molecular changes that drive childhood cancers. Investigators form a collaborative network to facilitate discovery of molecular targets and translate those findings into the clinic.

     http://ocg.cancer.gov/programs/target  

     

    Genome Analysis Toolkit (GATK)

    The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

     http://www.broadinstitute.org/gatk/  

     

    SAMtools

    SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

     http://samtools.sourceforge.net/