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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 165
2017 131
2018 125
2019 179
2020 138
2021 2
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1,423 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 …
Analysis of ChIP-seq Data in R/Bioconductor.
de Santiago I, Carroll T. de Santiago I, et al. Methods Mol Biol. 2018;1689:195-226. doi: 10.1007/978-1-4939-7380-4_17. Methods Mol Biol. 2018. PMID: 29027176
Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. This chapter provides an overview of the methods available to analyze ChIP-seq data based primarily on software packages from the open-source …
Over the last years, an array of R/Bioconductor tools has been developed allowing researchers to process and analyze ChIP-seq data. T …
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 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 …
Visualization of proteomics data using R and bioconductor.
Gatto L, Breckels LM, Naake T, Gibb S. Gatto L, et al. Proteomics. 2015 Apr;15(8):1375-89. doi: 10.1002/pmic.201400392. Proteomics. 2015. PMID: 25690415 Free PMC article. Review.
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. ...
This article describes a computational workflow for low-level analyses of scRNA-seq data, based primarily on software packages from the open …
CAGEfightR: analysis of 5'-end data using R/Bioconductor.
Thodberg M, Thieffry A, Vitting-Seerup K, Andersson R, Sandelin A. Thodberg M, et al. BMC Bioinformatics. 2019 Oct 4;20(1):487. doi: 10.1186/s12859-019-3029-5. BMC Bioinformatics. 2019. PMID: 31585526 Free PMC article.
CAGEfightR is implemented using standard Bioconductor classes, making it easy to learn, use and combine with other Bioconductor packages, for example popular differential expression tools such as limma, DESeq2 and edgeR. ...CAGEfightR is freely available via Bioc …
CAGEfightR is implemented using standard Bioconductor classes, making it easy to learn, use and combine with other Bioconductor …
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor.
Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD. Anders S, et al. Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. Epub 2013 Aug 22. Nat Protoc. 2013. PMID: 23975260
This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on the free open-source R language and Bioconductor software and, in particular, on two widely used tools, DESeq and edgeR. ...
This protocol presents a state-of-the-art computational and statistical RNA-seq differential expression analysis workflow largely based on t …
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ. Ou J, et al. BMC Genomics. 2018 Mar 1;19(1):169. doi: 10.1186/s12864-018-4559-3. BMC Genomics. 2018. PMID: 29490630 Free PMC article.
RESULTS: We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. ...The software, source code, and documentation are freely available as a Bioconductor …
RESULTS: We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quic …
TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.
Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H. Silva TC, et al. F1000Res. 2016 Jun 29;5:1542. doi: 10.12688/f1000research.8923.2. eCollection 2016. F1000Res. 2016. PMID: 28232861 Free PMC article.
The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. ...This workflow introduces the following Bioconductor packages: AnnotationHub, ChIPSeeker, ComplexHeatmap, pathview, ELMER, GAIA, …
The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data …
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization.
Yu G, He QY. Yu G, et al. Mol Biosyst. 2016 Feb;12(2):477-9. doi: 10.1039/c5mb00663e. Mol Biosyst. 2016. PMID: 26661513
ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses. ...The source code and documents of ReactomePA are freely available through Bioconductor (http://www.bioconductor.org/packag …
ReactomePA is an R/Bioconductor package providing enrichment analyses, including hypergeometric test and gene set enrichment analyses …
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