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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 2021-01-28T08:40:06-05:00.

Hicks SC, Liu R, Ni Y, Purdom E, Risso D. mbkmeans: Fast clustering for single cell data using mini-batch k-means. PLoS Comput Biol, 17(1), pp. e1008625. doi:10.1371/journal.pcbi.1008625 (26 January 2021)
Wang Q, Huang J, Chen X, Wang J, Fang F. Transcriptomic markers in pediatric septic shock prognosis: an integrative analysis of gene expression profiles. Braz J Med Biol Res, 54(3), pp. e10152. doi:10.1590/1414-431X202010152 (25 January 2021)
Mangiola S, Molania R, Dong R, Doyle MA, Papenfuss AT. tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biol, 22(1), pp. 42. doi:10.1186/s13059-020-02233-7 (22 January 2021)
Johnson WE, Odom A, Cintron C, Muthaiah M, Knudsen S, Joseph N, Babu S, Lakshminarayanan S, Jenkins DF, Zhao Y, Nankya E, Horsburgh CR, Roy G, Ellner J, Sarkar S, Salgame P, Hochberg NS. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis, 21(1), pp. 106. doi:10.1186/s12879-020-05598-z (22 January 2021)
Skinnider MA, Cai C, Stacey RG, Foster LJ. PrInCE: an R/bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data. Bioinformatics. doi:10.1093/bioinformatics/btab022 (20 January 2021)
Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI. Compression of quantification uncertainty for scRNA-seq counts. Bioinformatics. doi:10.1093/bioinformatics/btab001 (20 January 2021)
Choudhari JK, Verma MK, Choubey J, Sahariah BP. Investigation of MicroRNA and transcription factor mediated regulatory network for silicosis using systems biology approach. Sci Rep, 11(1), pp. 1265. doi:10.1038/s41598-020-77636-4 (14 January 2021)
Ruiz-Deya G, Matta J, Encarnación-Medina J, Ortiz-Sanchéz C, Dutil J, Putney R, Berglund A, Dhillon J, Kim Y, Park JY. Differential DNA Methylation in Prostate Tumors from Puerto Rican Men. Int J Mol Sci, 22(2). doi:10.3390/ijms22020733 (13 January 2021)
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics, 19(12), pp. 2115-2125. doi:10.1074/mcp.TIR120.002155 (12 January 2021)
Chen X, Ashoor H, Musich R, Wang J, Zhang M, Zhang C, Lu M, Li S. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. Sci Rep, 11(1), pp. 376. doi:10.1038/s41598-020-79627-x (11 January 2021)
Morante-Palacios O, Ballestar E. shinyÉPICo: A graphical pipeline to analyze Illumina DNA methylation arrays. Bioinformatics. doi:10.1093/bioinformatics/btaa1095 (8 January 2021)
Bhattacharya S, Barseghyan H, Délot EC, Vilain E. nanotatoR: a tool for enhanced annotation of genomic structural variants. BMC Genomics, 22(1), pp. 10. doi:10.1186/s12864-020-07182-w (6 January 2021)
Moulos P. recoup: flexible and versatile signal visualization from next generation sequencing. BMC Bioinformatics, 22(1), pp. 2. doi:10.1186/s12859-020-03902-x (6 January 2021)
Haselimashhadi H, Mason JC, Mallon AM, Smedley D, Meehan TF, Parkinson H. OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data. PLoS One, 15(12), pp. e0242933. doi:10.1371/journal.pone.0242933 (30 December 2020)
Appunni S, Rubens M, Ramamoorthy V, Sharma H, Singh AK, Swarup V, Singh HN. Differentially Expressed Genes and Their Clinical Significance in Ischaemic Stroke: An In-Silico Study. Malays J Med Sci, 27(6), pp. 53-67. doi:10.21315/mjms2020.27.6.6 (29 December 2020)
Zhang Y, Wang Z, Zhang Y, Tong H, Zhang Y, Lu T. Potential Mechanisms for Traditional Chinese Medicine in Treating Airway Mucus Hypersecretion Associated With Coronavirus Disease 2019. Front Mol Biosci, 7, pp. 577285. doi:10.3389/fmolb.2020.577285 (14 December 2020)
Huang T, Choi M, Tzouros M, Golling S, Pandya NJ, Banfai B, Dunkley T, Vitek O. MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures. Mol Cell Proteomics, 19(10), pp. 1706-1723. doi:10.1074/mcp.RA120.002105 (25 November 2020)
Zhu Y, Orre LM, Zhou Tran Y, Mermelekas G, Johansson HJ, Malyutina A, Anders S, Lehtiö J. DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis. Mol Cell Proteomics, 19(6), pp. 1047-1057. doi:10.1074/mcp.TIR119.001646 (23 November 2020)
Choudhary S, Anand R, Pradhan D, Bastia B, Kumar SN, Singh H, Puri P, Thomas G, Jain AK. Transcriptomic landscaping of core genes and pathways of mild and severe psoriasis vulgaris. Int J Mol Med, 47(1), pp. 219-231. doi:10.3892/ijmm.2020.4771 (27 October 2020)
Nieuwenhuis TO, Halushka MK. HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas. F1000Res, 9, pp. 1210. doi:10.12688/f1000research.26771.1 (8 October 2020)

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