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http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html
An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input.
Proper citation: VirusSeq (RRID:SCR_005206) Copy
http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview
A Java application to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns. SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on their server or can be installed locally to analyze your own mRNA-Seq data.
Proper citation: SpliceSeq (RRID:SCR_005267) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
