Detecting differential transcript usage across multiple conditions for RNA-seq data based on the smoothed LDA model

doi:10.1007/s11704-020-9348-x

Front. Comput. Sci.

2021, Vol. 15

Issue (3) : 153319 https://doi.org/10.1007/s11704-020-9348-x

LETTER

Detecting differential transcript usage across multiple conditions for RNA-seq data based on the smoothed LDA model

Jing LI^1,², Xuejun LIU^1,²(

), Daoqiang ZHANG^1,²

¹. 1College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing 211106, China
². 2Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210023, China

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Corresponding Author(s): Xuejun LIU

Just Accepted Date: 04 March 2020 Issue Date: 24 December 2020

Cite this article:

Jing LI,Xuejun LIU,Daoqiang ZHANG. Detecting differential transcript usage across multiple conditions for RNA-seq data based on the smoothed LDA model[J]. Front. Comput. Sci., 2021, 15(3): 153319.

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https://academic.hep.com.cn/fcs/EN/10.1007/s11704-020-9348-x
https://academic.hep.com.cn/fcs/EN/Y2021/V15/I3/153319

1	J E Hooper. A survey of software for genome-wide discovery of differential splicing in RNA-Seq data. Human Genomics, 2014, 8(1): 3 https://doi.org/10.1186/1479-7364-8-3
2	X Liu, X Shi, C Chen, L Zhang. Improving RNA-Seq expression estimation by modeling isoform-and exon-specific read sequencing rate. BMC Bioinformatics, 2015, 16(1): 332 https://doi.org/10.1186/s12859-015-0750-6
3	D M Blei, A Y Ng, M I Jordan. Latent dirichlet allocation. Journal of Machine Learning Research, 2003, 3(Jan): 993–1022
4	S Anders, A Reyes, W Huber. Detecting differential usage of exons from RNA-seq data. Genome Research, 2012, 22(10): 2008–2017 https://doi.org/10.1101/gr.133744.111
5	J L Trincado, J C Entizne, G Hysenaj, B Singh, M Skalic, D J Elliott, E Eyras. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biology, 2018, 19(1): 40 https://doi.org/10.1186/s13059-018-1417-1
6	C Trapnell, A Roberts, L Goff, G Pertea, D Kim, D R Kelley, H Pimentel, S L Salzberg, J L Rinn, L Pachter. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 2012, 7(3): 562 https://doi.org/10.1038/nprot.2012.016

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