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
Software interface: Command-line user interface; Workbench
Language: C++;C
Operating system: Linux; Mac OS X
License: Boost Software License v1

Cost

Version name: 2.2.1

Maturity:

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