Abstract
The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation.
Original language | English |
---|---|
Pages (from-to) | 1839-1855 |
Number of pages | 17 |
Journal | RNA (New York, N.Y.) |
Volume | 29 |
Issue number | 12 |
DOIs | |
Publication status | Published - Dec 2023 |
Keywords
- Benchmarking
- Polyadenylation
- RNA-Seq
- RNA/genetics
- Sequence Analysis, RNA/methods
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In: RNA (New York, N.Y.), Vol. 29, No. 12, 12.2023, p. 1839-1855.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data
AU - Bryce-Smith, Sam
AU - Burri, Dominik
AU - Gazzara, Matthew R
AU - Herrmann, Christina J
AU - Danecka, Weronika
AU - Fitzsimmons, Christina M
AU - Wan, Yuk Kei
AU - Zhuang, Farica
AU - Fansler, Mervin M
AU - Fernández, José M
AU - Ferret, Meritxell
AU - Gonzalez-Uriarte, Asier
AU - Haynes, Samuel
AU - Herdman, Chelsea
AU - Kanitz, Alexander
AU - Katsantoni, Maria
AU - Marini, Federico
AU - McDonnel, Euan
AU - Nicolet, Ben
AU - Poon, Chi-Lam
AU - Rot, Gregor
AU - Schärfen, Leonard
AU - Wu, Pin-Jou
AU - Yoon, Yoseop
AU - Barash, Yoseph
AU - Zavolan, Mihaela
AU - Nicolet, B.P.
N1 - Funding Information: We thank the RNA Society for making the hackathon possible and bringing together people from various disciplines. We thank the OpenEBench platform (https://openebench.bsc.es/) for hosting the APAeval benchmark. We thank OEB members Anna Redondo, Laura Portell, Laura Rodriguez-Navas, and Salvador Capella for help and contributions. We thank Seqera Labs (https://seqera.io/) for kindly hosting a workshop regarding the use of Nextflow and Nextflow Tower during the RNA Society 2021 meeting, and Amazon Web Services for providing us with credits for the use of their cloud platform. We are grateful to host the source code on the iRNA COSI (https:// irnacosi .org/) GitHub account. S.B.-S. was supported by a UK Motor Neurone Disease Association and Masonic Charitable Foundation PhD Studentship (893-792). C.M.F. was partially supported by a postdoctoral fellowship from the American Cancer Society (PF-19-157-01-RMC). M.R.G. was supported by the Blavatnik Family Fellowship in Biomedical Research and by NHLBI of the National Institutes of Health (NIH) under award number F31 HL162546. A.G.-U. was supported by the The Emerging Human Brain Cluster (Clúster Emergent del Cervell Humà – CECH) project, number 001-P-001682, 50% cofunded by the European Regional Development Fund of the European Union (Programa Operatiu FEDER Catalunya 2014–2020), with the support of the Catalan Government. Y.K.W. was supported by the Singapore International Graduate Award. OpenEBench is partly funded by the Horizon 2020 ELIXIR-CONVERGE programme, grant agreement number 871075. The work of Y.B. was supported by R01 GM128096, R01 GM147739, and R01 LM013437. D.B. and C.J.H. were partially supported by the Swiss National Science Foundation grant number 310030_189063 to M.Z. Publisher Copyright: © 2023 Bryce-Smith et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
PY - 2023/12
Y1 - 2023/12
N2 - The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation.
AB - The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is an increasing need for benchmarks, and for the provision of infrastructure for continuous method evaluation.
KW - Benchmarking
KW - Polyadenylation
KW - RNA-Seq
KW - RNA/genetics
KW - Sequence Analysis, RNA/methods
UR - http://www.scopus.com/inward/record.url?scp=85177103265&partnerID=8YFLogxK
U2 - https://doi.org/10.1261/rna.079849.123
DO - https://doi.org/10.1261/rna.079849.123
M3 - Article
C2 - 37816550
SN - 1355-8382
VL - 29
SP - 1839
EP - 1855
JO - RNA (New York, N.Y.)
JF - RNA (New York, N.Y.)
IS - 12
ER -