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Page 1
Near-optimal probabilistic RNA-seq quantification.
Bray NL, Pimentel H, Melsted P, Pachter L. Bray NL, et al. Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4. Nat Biotechnol. 2016. PMID: 27043002
kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq.
Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. Sullivan DK, et al. Among authors: bray nl. bioRxiv [Preprint]. 2024 Jan 23:2023.11.21.568164. doi: 10.1101/2023.11.21.568164. bioRxiv. 2024. Update in: Nat Protoc. 2024 Oct 10. doi: 10.1038/s41596-024-01057-0 PMID: 38045414 Free PMC article. Updated. Preprint.
The impact of package selection and versioning on single-cell RNA-seq analysis.
Rich JM, Moses L, Einarsson PH, Jackson K, Luebbert L, Booeshaghi AS, Antonsson S, Sullivan DK, Bray N, Melsted P, Pachter L. Rich JM, et al. bioRxiv [Preprint]. 2024 Apr 11:2024.04.04.588111. doi: 10.1101/2024.04.04.588111. bioRxiv. 2024. PMID: 38617255 Free PMC article. Preprint.
Pseudoalignment for metagenomic read assignment.
Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Schaeffer L, et al. Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106. Bioinformatics. 2017. PMID: 28334086 Free PMC article.
27 results