CIDANE swMATH ID: 43284 Software Authors: Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W Klau Description: CIDANE: comprehensive isoform discovery and abundance estimation. We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity and precision than existing tools. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms. CIDANE supports the integrated analysis of RNA-seq and additional gene-boundary data and recovers splice junctions that are invisible to other methods. CIDANE is available at http://ccb.jhu.edu/software/cidane/. Homepage: http://ccb.jhu.edu/software/cidane/ Source Code: https://bitbucket.org/canzar/cidane/src/master/ Related Software: HISAT; Salmon; Gurobi; MultiTrans; Scallop2; ShoRAH; SSP; StringTie; RefShannon; IsoLasso; MFD-ILP; CLIIQ; RNASeqReadSimulator; GitHub; Ipopt; CPLEX; MotifCut; SageMath; NetworkX Cited in: 2 Documents all top 5 Cited by 7 Authors 1 Calude, Cristian S. 1 Dias, Fernando H. C. 1 Dinneen, Michael J. 1 Hua, Richard 1 Mumey, Brendan 1 Tomescu, Alexandru Ioan 1 Williams, Lucia Cited in 1 Serial 1 Journal of Membrane Computing Cited in 3 Fields 2 Operations research, mathematical programming (90-XX) 1 Computer science (68-XX) 1 Biology and other natural sciences (92-XX) Citations by Year