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📖 Bioconductor Publications

Publications

This is a select list of featured and recent publications that cite Bioconductor, along with select books, book chapters, and original Bioconductor technical reports.

Featured

Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 1:kxab030. doi: 10.1093/biostatistics/kxab030. Epub ahead of print. PMID: 34467372.
Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun. 2022 Jun 27;13(1):3695. doi: 10.1038/s41467-022-31411-3. PMID: 35760813; PMCID: PMC9237024
Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O'Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022 Jan 12;2(1):100085. doi: 10.1016/j.xgen.2021.100085. Epub 2022 Jan 13. PMID: 35199087; PMCID: PMC8863334
He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11. PMID: 35277707; PMCID: PMC8933848

Recent

10 most recent PubMed and PubMed Central citations mentioning "*Bioconductor*". For a complete list, go to PubMed and PubMed Central. Last updated 2024-06-13T00:00:08-04:00.

Guazzini M, Reisach AG, Weichwald S, Seiler C. spillR: Spillover compensation in mass cytometry data. Bioinformatics. doi:10.1093/bioinformatics/btae337 (7 June 2024)
Li J, Li W, Peng X, Li X, Zhao S, Wang H, Ma Y. Genetic basis of phenotypic convergence in pig terminal sires using pathway-based selection signature detection methods. Anim Genet. doi:10.1111/age.13454 (3 June 2024)
Grentner A, Ragueneau E, Gong C, Prinz A, Gansberger S, Oyarzun I, Hermjakob H, Griss J. ReactomeGSA: new features to simplify public data reuse. Bioinformatics, 40(6). doi:10.1093/bioinformatics/btae338 (3 June 2024)
Davis ES, Parker SM, Kramer NE, Flores JP, Kiran M, Phanstiel DH. Mariner: Explore the Hi-Cs. Bioinformatics. doi:10.1093/bioinformatics/btae352 (30 May 2024)
Almeida-Silva F, Prost-Boxoen L, Van de Peer Y. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors. New Phytol. doi:10.1111/nph.19862 (27 May 2024)
Roux de Bézieux H, Street K, Fischer S, Van den Berge K, Chance R, Risso D, Gillis J, Ngai J, Purdom E, Dudoit S. Improving replicability in single-cell RNA-Seq cell type discovery with Dune. BMC Bioinformatics, 25(1), pp. 198. doi:10.1186/s12859-024-05814-6 (24 May 2024)
Hutchison WJ, Keyes TJ, Crowell HL, Serizay J, Soneson C, Davis ES, Sato N, Moses L, Tarlinton B, Nahid AA, Kosmac M, Clayssen Q, Yuan V, Mu W, Park JE, Mamede I, Ryu MH, Axisa PP, Paiz P, Poon CL, Tang M, Gottardo R, Morgan M, Lee S, Lawrence M, Hicks SC, Nolan GP, Davis KL, Papenfuss AT, Love MI, Mangiola S. The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv. doi:10.1101/2023.09.10.557072 (22 May 2024)
Oh S, Gravel-Pucillo K, Ramos M, Davis S, Carey V, Morgan M, Waldron L. AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines. Res Sq. doi:10.21203/rs.3.rs-4370115/v1 (15 May 2024)
Basmadjian RB, O'Sullivan DE, Quan ML, Lupichuk S, Xu Y, Cheung WY, Brenner DR. The Association between Mutational Signatures and Clinical Outcomes among Patients with Early-Onset Breast Cancer. Genes (Basel), 15(5). doi:10.3390/genes15050592 (7 May 2024)
Loubaton R, Champagnat N, Vallois P, Vallat L. MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions. Bioinformatics, 40(5). doi:10.1093/bioinformatics/btae315 (2 May 2024)

Bioconductor Project Papers

Bioconductor key papers and technical reports.
Papers
Huber et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 2015, 12:115-121.
Initial Bioconductor Technical Reports
Bioconductor Core (November 2002) Bioconductor: Assessment of Current Progress


Books

A selection of Bioconductor releated books, book chapters, and online books.


Books
Landmark Bioconductor Book     R Programming for Bioinformatics     Bioconductor Case Studies


Book Chapters
Analyzing biological data using R: methods for graphs and networks


Online Books


Other

F1000 Research Channel