Exact transcript quantification over splice graphs

DOI10.4230/LIPICS.WABI.2020.12zbMATH Open1515.92047MaRDI QIDQ6487643FDOQ6487643

Authors: Cong Ma, Hongyu Zheng, Carl Kingsford 

Publication date: 7 February 2023

Recommendations

• Deconvolution of base pair level RNA-seq read counts for quantification of transcript expression levels
• Statistical modeling of RNA-Seq data
• Quantifying alternative splicing from paired-end RNA-sequencing data
• A penalized likelihood approach for robust estimation of isoform expression
• Improved variational Bayes inference for transcript expression estimation

zbMATH Keywords

RNA-seqnetwork flowalternative splicingsplice graphtranscript quantification

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Efficient string matching

Cited In (7)

• A practical fpt algorithm for F<scp>low</scp> D<scp>ecomposition</scp> and transcript assembly
• Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth.
• Safety and completeness in flow decompositions for RNA assembly
• Deconvolution of base pair level RNA-seq read counts for quantification of transcript expression levels
• Quantifying alternative splicing from paired-end RNA-sequencing data
• Transcript abundance estimation and the laminar packing problem
• Yanagi: transcript segment library construction for RNA-seq quantification

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