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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1996 1
2000 1
2003 7
2004 13
2005 19
2006 30
2007 44
2008 52
2009 62
2010 51
2011 70
2012 81
2013 109
2014 118
2015 151
2016 166
2017 131
2018 126
2019 180
2020 170
2021 178
2022 68
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1,685 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 …
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 …
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 …
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
Lun AT, McCarthy DJ, Marioni JC. Lun AT, et al. F1000Res. 2016 Aug 31;5:2122. doi: 10.12688/f1000research.9501.2. eCollection 2016. F1000Res. 2016. PMID: 27909575 Free PMC article.
This article describes a computational workflow for low-level analyses of scRNA-seq data, based primarily on software packages from the open-source Bioconductor project. It covers basic steps including quality control, data exploration and normalization, as well as more co …
This article describes a computational workflow for low-level analyses of scRNA-seq data, based primarily on software packages from the open …
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
Meng J, Lu Z, Liu H, Zhang L, Zhang S, Chen Y, Rao MK, Huang Y. Meng J, et al. Methods. 2014 Oct 1;69(3):274-81. doi: 10.1016/j.ymeth.2014.06.008. Epub 2014 Jun 27. Methods. 2014. PMID: 24979058 Free PMC article.
We therein provide here a detailed and easy-to-use protocol of using exomePeak R/Bioconductor package along with other software programs for analysis of MeRIP-Seq data, which covers raw reads alignment, RNA methylation site detection, motif discovery, differential RNA meth …
We therein provide here a detailed and easy-to-use protocol of using exomePeak R/Bioconductor package along with other software progr …
Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines.
Hu Q, Hutson A, Liu S, Morgan M, Liu Q. Hu Q, et al. Bioinformatics. 2021 Mar 27;37(19):3351-2. doi: 10.1093/bioinformatics/btab208. Online ahead of print. Bioinformatics. 2021. PMID: 33772584 Free PMC article.
AVAILABILITY: Project website: https://rcwl.org (Rcwl: https://bioconductor.org/packages/Rcwl; RcwlPipelines: https://bioconductor.org/packages/RcwlPipelines). ...
AVAILABILITY: Project website: https://rcwl.org (Rcwl: https://bioconductor.org/packages/Rcwl; RcwlPipelines: https://bioconductor
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME. Su S, et al. PLoS Comput Biol. 2021 Oct 25;17(10):e1009524. doi: 10.1371/journal.pcbi.1009524. eCollection 2021 Oct. PLoS Comput Biol. 2021. PMID: 34695109 Free PMC article.
A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of R/Bioconductor tools for the effective visualization of nanopore methylation profiles between samples from different experimental gr …
A key benefit of long-read nanopore sequencing technology is the ability to detect modified DNA bases, such as 5-methylcytosine. The lack of …
TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis.
Patel K, Chandrasegaran S, Clark IM, Proctor CJ, Young DA, Shanley DP. Patel K, et al. Bioinformatics. 2021 May 16;37(20):3604-9. doi: 10.1093/bioinformatics/btab377. Online ahead of print. Bioinformatics. 2021. PMID: 33993215 Free PMC article.
AVAILABILITY AND IMPLEMENTATION: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGeN) and requires R v4.0.2 or newer and BiocManager v3.12 or newer. ...
AVAILABILITY AND IMPLEMENTATION: TimiRGeN is available for download on Bioconductor (https://bioconductor.org/packages/TimiRGe …
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves.
Cardoso MA, Rizzardi LEA, Kume LW, Groeneveld C, Trefflich S, Morais DAA, Dalmolin RJS, Ponder BAJ, Meyer KB, Castro MAA. Cardoso MA, et al. Bioinformatics. 2021 Dec 2:btab819. doi: 10.1093/bioinformatics/btab819. Online ahead of print. Bioinformatics. 2021. PMID: 34864914
Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especially for large trees. RESULTS: Here we present TreeAndLeaf, an R/Bioconductor package that implements a hybrid layout strategy to repres …
Although efficient to represent hierarchical relations, it provides limited space for displaying information on the leaf elements, especiall …
Interpretation of differential gene expression results of RNA-seq data: review and integration.
McDermaid A, Monier B, Zhao J, Liu B, Ma Q. McDermaid A, et al. Brief Bioinform. 2019 Nov 27;20(6):2044-2054. doi: 10.1093/bib/bby067. Brief Bioinform. 2019. PMID: 30099484 Free PMC article. Review.
Here we reviewed DGE results analysis from a functional point of view for various visualizations. We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich visualizations for the interpretatio …
Here we reviewed DGE results analysis from a functional point of view for various visualizations. We also provide an R/Bioconductor p …
1,685 results