cufflinks (cloudIFB)
cufflinks (cloudIFB) is a workflow tool for various different analyses in RNA-seq data.
Topic
RNA-Seq; Transcriptomics
Details
- Operation: RNA-seq time series data analysis; Transcriptome assembly; Sequence comparison; DNA transcription; Aggregation; RNA-seq read count analysis; Gene expression analysis; Gene expression comparison; Standardisation and normalisation
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- Software interface: Command-line user interface; Workbench
- Language: C++;C
- Operating system: Linux; Mac OS X
- License: Boost Software License v1 Cost: Free
- Version name: 2.2.1 Maturity: Mature
- Credit: The National Institutes of Health (NIH), the Beckman Foundation, Bren Foundation, Moore Foundation (Cell Center Program), the Miller Research Institute.
- Contact: tophat.cufflinks _at_ gmail.com
- Collection: -
Publications
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation." Nat Biotechnol. 2010 May;28(5):511-5. https://doi.org/10.1038/nbt.1621
PMID: 20436464
PMCID: PMC3146043
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