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http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
Proper citation: Cufflinks (RRID:SCR_014597) Copy
http://compbio.iupui.edu/group/6/pages/alteventfinder
Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only.
Proper citation: Alt Event Finder (RRID:SCR_001846) Copy
http://cufflinks.cbcb.umd.edu/
Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.
Proper citation: Cuffdiff (RRID:SCR_001647) 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.
