Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth.

DOI10.4230/LIPICS.WABI.2021.4MaRDI QIDQ6133864zbMATH OpenOpenAlexFDO

Authors Jason Fan, R. Patro

Publication date 24 July 2023

Full work available at URL https://drops.dagstuhl.de/opus/volltexte/2021/14357/pdf/LIPIcs-WABI-2021-4.pdf/

zbMATH Keywords

model selectionRNA-seqtranscript abundance estimation

Mathematics Subject Classification ID

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

Recommendations

• Deconvolution of base pair level RNA-seq read counts for quantification of transcript expression levels
• Statistical modeling of RNA-Seq data
• Improved variational Bayes inference for transcript expression estimation
• A penalized likelihood approach for robust estimation of isoform expression
• Exact transcript quantification over splice graphs

Cited in

(2)

• Discrepancy between mRNA and protein abundance: insight from information retrieval process in computers
• Transcript abundance estimation and the laminar packing problem

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