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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. Among authors: booeshaghi as. bioRxiv [Preprint]. 2024 Apr 11:2024.04.04.588111. doi: 10.1101/2024.04.04.588111. bioRxiv. 2024. PMID: 38617255 Free PMC article. Preprint.
A machine-readable specification for genomics assays.
Booeshaghi AS, Chen X, Pachter L. Booeshaghi AS, et al. Bioinformatics. 2024 Mar 29;40(4):btae168. doi: 10.1093/bioinformatics/btae168. Bioinformatics. 2024. PMID: 38579259 Free PMC article.
Quantifying orthogonal barcodes for sequence census assays.
Booeshaghi AS, Min KHJ, Gehring J, Pachter L. Booeshaghi AS, et al. Bioinform Adv. 2023 Dec 20;4(1):vbad181. doi: 10.1093/bioadv/vbad181. eCollection 2024. Bioinform Adv. 2023. PMID: 38213823 Free PMC article.
Universal preprocessing of single-cell genomics data.
Booeshaghi AS, Sullivan DK, Pachter L. Booeshaghi AS, et al. bioRxiv [Preprint]. 2023 Sep 15:2023.09.14.543267. doi: 10.1101/2023.09.14.543267. bioRxiv. 2023. PMID: 37745572 Free PMC article. Preprint.
A machine-readable specification for genomics assays.
Booeshaghi AS, Chen X, Pachter L. Booeshaghi AS, et al. bioRxiv [Preprint]. 2023 Jul 18:2023.03.17.533215. doi: 10.1101/2023.03.17.533215. bioRxiv. 2023. PMID: 36993635 Free PMC article. Updated. Preprint.
Metadata retrieval from sequence databases with ffq.
Gálvez-Merchán Á, Min KHJ, Pachter L, Booeshaghi AS. Gálvez-Merchán Á, et al. Among authors: booeshaghi as. Bioinformatics. 2023 Jan 1;39(1):btac667. doi: 10.1093/bioinformatics/btac667. Bioinformatics. 2023. PMID: 36610997 Free PMC article.
18 results