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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.
MAVID multiple alignment server.
Bray N, Pachter L. Bray N, et al. Nucleic Acids Res. 2003 Jul 1;31(13):3525-6. doi: 10.1093/nar/gkg623. Nucleic Acids Res. 2003. PMID: 12824358 Free PMC article.
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
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.
Expression reflects population structure.
Brown BC, Bray NL, Pachter L. Brown BC, et al. Among authors: bray nl. PLoS Genet. 2018 Dec 19;14(12):e1007841. doi: 10.1371/journal.pgen.1007841. eCollection 2018 Dec. PLoS Genet. 2018. PMID: 30566439 Free PMC article.
27 results