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Year Number of Results
1996 1
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2,076 results

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Page 1
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Robinson MD, McCarthy DJ, Smyth GK. Robinson MD, et al. Bioinformatics. 2010 Jan 1;26(1):139-40. doi: 10.1093/bioinformatics/btp616. Epub 2009 Nov 11. Bioinformatics. 2010. PMID: 19910308 Free PMC article.
One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for …
One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that coun …
clusterProfiler: an R package for comparing biological themes among gene clusters.
Yu G, Wang LG, Han Y, He QY. Yu G, et al. OMICS. 2012 May;16(5):284-7. doi: 10.1089/omi.2011.0118. Epub 2012 Mar 28. OMICS. 2012. PMID: 22455463 Free PMC article.
The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html....
The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are free …
Bioconductor's Computational Ecosystem for Genomic Data Science in Cancer.
Ramos M, Shepherd L, Sheffield NC, Mahmoud A, Pagès H, Wokaty A, Righelli D, Risso D, Davis S, Oh S, Waldron L, Morgan M, Carey V. Ramos M, et al. Methods Mol Biol. 2025;2932:1-46. doi: 10.1007/978-1-0716-4566-6_1. Methods Mol Biol. 2025. PMID: 40779102 Review.
The Bioconductor project enters its third decade with over two thousand packages for genomic data science, over 100,000 annotation and experiment resources, and a global system for convenient distribution to researchers. ...This report provides an overview of cancer genomi …
The Bioconductor project enters its third decade with over two thousand packages for genomic data science, over 100,000 annotation an …
Using R and Bioconductor in Clinical Genomics and Transcriptomics.
Sepulveda JL. Sepulveda JL. J Mol Diagn. 2020 Jan;22(1):3-20. doi: 10.1016/j.jmoldx.2019.08.006. Epub 2019 Oct 9. J Mol Diagn. 2020. PMID: 31605800 Free article. Review.
Software tools written in the R statistical language and, in particular, the set of tools available in the Bioconductor repository are widely used in research bioinformatics; and these frameworks offer several advantages for use in clinical bioinformatics, including the br …
Software tools written in the R statistical language and, in particular, the set of tools available in the Bioconductor repository ar …
Using clusterProfiler to characterize multiomics data.
Xu S, Hu E, Cai Y, Xie Z, Luo X, Zhan L, Tang W, Wang Q, Liu B, Wang R, Xie W, Wu T, Xie L, Yu G. Xu S, et al. Nat Protoc. 2024 Nov;19(11):3292-3320. doi: 10.1038/s41596-024-01020-z. Epub 2024 Jul 17. Nat Protoc. 2024. PMID: 39019974 Review.
In all cases, the computational steps can be completed within ~2 min. clusterProfiler is released through the Bioconductor project and can be accessed via https://bioconductor.org/packages/clusterProfiler/ ....
In all cases, the computational steps can be completed within ~2 min. clusterProfiler is released through the Bioconductor project an …
monaLisa: an R/Bioconductor package for identifying regulatory motifs.
Machlab D, Burger L, Soneson C, Rijli FM, Schübeler D, Stadler MB. Machlab D, et al. Bioinformatics. 2022 Apr 28;38(9):2624-2625. doi: 10.1093/bioinformatics/btac102. Bioinformatics. 2022. PMID: 35199152 Free PMC article.
The package can be easily integrated with other Bioconductor packages and enables seamless motif analyses without any software dependencies outside of R. AVAILABILITY AND IMPLEMENTATION: monaLisa is implemented in R and available on Bioconductor at https://biocon …
The package can be easily integrated with other Bioconductor packages and enables seamless motif analyses without any software depend …
Synaptome.db: a bioconductor package for synaptic proteomics data.
Sorokina O, Sorokin A, Armstrong JD. Sorokina O, et al. Bioinform Adv. 2022 Nov 12;2(1):vbac086. doi: 10.1093/bioadv/vbac086. eCollection 2022. Bioinform Adv. 2022. PMID: 36699346 Free PMC article.
Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-depth data analysis from within the Bioconductor environment. ...AVAILABILITY AND IMPLEMENTATION: The package Synaptome.db is part of …
Here, we describe programmatic access to the dataset via the R/Bioconductor package Synaptome.db, which enables convenient and in-dep …
BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data.
Eagles NJ, Wilton R, Jaffe AE, Collado-Torres L. Eagles NJ, et al. BMC Bioinformatics. 2023 Sep 13;24(1):340. doi: 10.1186/s12859-023-05461-3. BMC Bioinformatics. 2023. PMID: 37704947 Free PMC article.
In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipelines renders WGBS impractical or impossible to many researchers. RESULTS: We present BiocMAP, a Bioconductor-friendly methylation analys …
In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipeline …
Curated single cell multimodal landmark datasets for R/Bioconductor.
Eckenrode KB, Righelli D, Ramos M, Argelaguet R, Vanderaa C, Geistlinger L, Culhane AC, Gatto L, Carey V, Morgan M, Risso D, Waldron L. Eckenrode KB, et al. PLoS Comput Biol. 2023 Aug 25;19(8):e1011324. doi: 10.1371/journal.pcbi.1011324. eCollection 2023 Aug. PLoS Comput Biol. 2023. PMID: 37624866 Free PMC article.
The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes. ...We integrate data modalities via the MultiAssayExperiment Bioconductor class, doc …
The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability o …
2,076 results