Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with Isosceles
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DOI: 10.1038/s41467-024-51584-3
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- Kevin Lebrigand & Virginie Magnone & Pascal Barbry & Rainer Waldmann, 2020. "High throughput error corrected Nanopore single cell transcriptome sequencing," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
- Mamie Yu & Suresh K. Selvaraj & May M. Y. Liang-Chu & Sahar Aghajani & Matthew Busse & Jean Yuan & Genee Lee & Franklin Peale & Christiaan Klijn & Richard Bourgon & Joshua S. Kaminker & Richard M. Nev, 2015. "A resource for cell line authentication, annotation and quality control," Nature, Nature, vol. 520(7547), pages 307-311, April.
- James M. McFarland & Brenton R. Paolella & Allison Warren & Kathryn Geiger-Schuller & Tsukasa Shibue & Michael Rothberg & Olena Kuksenko & William N. Colgan & Andrew Jones & Emily Chambers & Danielle , 2020. "Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
- Alison D. Tang & Cameron M. Soulette & Marijke J. van Baren & Kevyn Hart & Eva Hrabeta-Robinson & Catherine J. Wu & Angela N. Brooks, 2020. "Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
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