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Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Orchestrating single-cell analysis with Bioconductor. Nature Methods (2019) doi:10.1038/s41592-019-0654-x
Pasolli, E, et al. (2017) Accessible, curated metagenomic data through ExperimentHub Nature Methods 14, 1023–1024. doi:10.1038/nmeth.4468
Huber W, et al. (2015) Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115-121; doi:10.1038/nmeth.3252 (full-text free with registration).
Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLoS Comput Biol 9(8): e1003118. doi: 10.1371/journal.pcbi.1003118
Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2022-01-27T07:30:08-05:00.

Beeraka NM, Gu H, Xue N, Liu Y, Yu H, Liu J, Chen K, Nikolenko VN, Fan R. Testing lncRNAs signature as clinical stage-related prognostic markers in gastric cancer progression using TCGA database. Exp Biol Med (Maywood), pp. 15353702211067173. doi:10.1177/15353702211067173 (22 January 2022)
Roquencourt C, Grassin-Delyle S, Thévenot EA. ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath. Bioinformatics. doi:10.1093/bioinformatics/btac031 (19 January 2022)
Li Z, Feng H. A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data. Sci Rep, 12(1), pp. 910. doi:10.1038/s41598-021-04473-4 (18 January 2022)
Nguyen V, Griss J. scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data. BMC Bioinformatics, 23(1), pp. 44. doi:10.1186/s12859-022-04574-5 (17 January 2022)
Tao W, Radstake TRDJ, Pandit A. RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling. Commun Biol, 5(1), pp. 31. doi:10.1038/s42003-021-02991-5 (11 January 2022)
Buddham R, Chauhan S, Narad P, Mathur P. Reconstruction and exploratory analysis of mTORC1 signalling pathway and its applications to various diseases using Network based approach. J Microbiol Biotechnol, 32(3). doi:10.4014/jmb.2108.08007 (8 January 2022)
Prašnikar E, Kunej T, Gorenjak M, Potočnik U, Kovačič B, Knez J. Transcriptomics of receptive endometrium in women with sonographic features of adenomyosis. Reprod Biol Endocrinol, 20(1), pp. 2. doi:10.1186/s12958-021-00871-5 (3 January 2022)
Marini F, Ludt A, Linke J, Strauch K. GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data. BMC Bioinformatics, 22(1), pp. 610. doi:10.1186/s12859-021-04461-5 (23 December 2021)
Kariyawasam H, Su S, Voogd O, Ritchie ME, Law CW. Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0. NAR Genom Bioinform, 3(4), pp. lqab116. doi:10.1093/nargab/lqab116 (22 December 2021)
Rehman SU, Muhammad K, Novaes E, Que Y, Din A, Islam M, Porto ACM, Inamullah M, Sajid M, Ullah N, Iqsa S. Expression analysis of transcription factors in sugarcane during cold stress. Braz J Biol, 83, pp. e242603. doi:10.1590/1519-6984.242603 (20 December 2021)
Ustjanzew A, Desuki A, Ritzel C, Dolezilek AC, Wagner DC, Christoph J, Unberath P, Kindler T, Faber J, Marini F, Panholzer T, Paret C. cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board. BMC Med Inform Decis Mak, 21(1), pp. 358. doi:10.1186/s12911-021-01719-z (20 December 2021)
Jablonski KP, Pirkl M, Ćevid D, Bühlmann P, Beerenwinkel N. Identifying cancer pathway dysregulations using differential causal effects. Bioinformatics. doi:10.1093/bioinformatics/btab847 (20 December 2021)
Settino M, Cannataro M. Using MMRFBiolinks R-Package for Discovering Prognostic Markers in Multiple Myeloma. Methods Mol Biol, 2401, pp. 289-314. doi:10.1007/978-1-0716-1839-4_19 (14 December 2021)
Chicco D. geneExpressionFromGEO: An R Package to Facilitate Data Reading from Gene Expression Omnibus (GEO). Methods Mol Biol, 2401, pp. 187-194. doi:10.1007/978-1-0716-1839-4_12 (14 December 2021)
Guo J, Liu Y, Zhao P. Bioinformatic Analysis Identified Potentially Prognostic Long Noncoding RNAs and MicroRNAs for Gastric Cancer. Biomed Res Int, 2021, pp. 6683136. doi:10.1155/2021/6683136 (10 December 2021)
Li T, Zhang Y, Patil P, Johnson WE. Overcoming the impacts of two-step batch effect correction on gene expression estimation and inference. Biostatistics. doi:10.1093/biostatistics/kxab039 (10 December 2021)
Cardoso MA, Rizzardi LEA, Kume LW, Groeneveld C, Trefflich S, Morais DAA, Dalmolin RJS, Ponder BAJ, Meyer KB, Castro MAA. TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves. Bioinformatics. doi:10.1093/bioinformatics/btab819 (2 December 2021)
Mukherjee M, Goswami S. Identification of Key Deregulated RNA-Binding Proteins in Pancreatic Cancer by Meta-Analysis and Prediction of Their Role as Modulators of Oncogenesis. Front Cell Dev Biol, 9, pp. 713852. doi:10.3389/fcell.2021.713852 (29 November 2021)
Li J, Chen Z, Liao H, Zhong Y, Hua J, Su M, Li J, Xu J, Cui L, Cui Y. Anti-Osteogenic Effect of Danshensu in Ankylosing Spondylitis: An in Vitro Study Based on Integrated Network Pharmacology. Front Pharmacol, 12, pp. 772190. doi:10.3389/fphar.2021.772190 (25 November 2021)
Whalley C, Payne K, Domingo E, Blake A, Richman S, Brooks J, Batis N, Spruce R, S-Cort Consortium, Mehanna H, Nankivell P, Beggs AD. Ultra-Low DNA Input into Whole Genome Methylation Assays and Detection of Oncogenic Methylation and Copy Number Variants in Circulating Tumour DNA. Epigenomes, 5(1). doi:10.3390/epigenomes5010006 (19 February 2021)

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