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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 2020-05-30T12:20:06-04:00.

Carey VJ, Ramos M, Stubbs BJ, Gopaulakrishnan S, Oh S, Turaga N, Waldron L, Morgan M. Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale. JCO Clin Cancer Inform, 4, pp. 472-479. doi:10.1200/CCI.19.00111 (27 May 2020)
Wu JX, Pascovici D, Wu Y, Walker AK, Mirzaei M. Workflow for Rapidly Extracting Biological Insights from Complex, Multicondition Proteomics Experiments with WGCNA and PloGO2. J Proteome Res. doi:10.1021/acs.jproteome.0c00198 (22 May 2020)
Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L, Chen X. PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. Proteomics, pp. e1900409. doi:10.1002/pmic.201900409 (20 May 2020)
El-Kurdi A, Khalil GA, Khazen G, Khoueiry P. fcScan: a versatile tool to cluster combinations of sites using genomic coordinates. BMC Bioinformatics, 21(1), pp. 194. doi:10.1186/s12859-020-3536-4 (19 May 2020)
Youngblood H, Cai J, Drewry MD, Helwa I, Hu E, Liu S, Yu H, Mu H, Hu Y, Perkumas K, Aboobakar IF, Johnson WM, Stamer WD, Liu Y. Expression of mRNAs, miRNAs, and lncRNAs in Human Trabecular Meshwork Cells Upon Mechanical Stretch. Invest Ophthalmol Vis Sci, 61(5), pp. 2. doi:10.1167/iovs.61.5.2 (11 May 2020)
Chen S, Gao C, Wu Y, Huang Z. Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer. Front Pharmacol, 11, pp. 544. doi:10.3389/fphar.2020.00544 (8 May 2020)
Ishak M, Baharudin R, Rose IM, Sagap I, Mazlan L, Azman ZAM, Abu N, Jamal R, Lee LH, Mutalib NSA. Genome-Wide Open Chromatin Methylome Profiles in Colorectal Cancer. Biomolecules, 10(5). doi:10.3390/biom10050719 (5 May 2020)
Schlosser P, Knaus J, Schmutz M, Dohner K, Plass C, Bullinger L, Claus R, Binder H, Lubbert M, Schumacher M. Netboost: Boosting-supported Network Analysis Improves High-Dimensional Omics Prediction in Acute Myeloid Leukemia and Huntington's Disease. IEEE/ACM Trans Comput Biol Bioinform. doi:10.1109/TCBB.2020.2983010 (1 May 2020)
Ren X, Kuan PF. Negative binomial additive model for RNA-Seq data analysis. BMC Bioinformatics, 21(1), pp. 171. doi:10.1186/s12859-020-3506-x (1 May 2020)
Andresen AMS, Boudinot P, Gjøen T. Kinetics of transcriptional response against poly (I:C) and infectious salmon anemia virus (ISAV) in Atlantic salmon kidney (ASK) cell line. Dev Comp Immunol, 110, pp. 103716. doi:10.1016/j.dci.2020.103716 (29 April 2020)
Bergenstråhle J, Bergenstråhle L, Lundeberg J. SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation. BMC Bioinformatics, 21(1), pp. 161. doi:10.1186/s12859-020-3489-7 (29 April 2020)
Jia L, Liu N, Huang F, Zhou Z, He X, Li H, Wang Z, Yao W. intansv: an R package for integrative analysis of structural variations. PeerJ, 8, pp. e8867. doi:10.7717/peerj.8867 (28 April 2020)
Smith-McCune K, Thomas R, Averbach S, Seidman D, Takeda M, Houshdaran S, Giudice LC. Differential Effects of the Hormonal and Copper Intrauterine Device on the Endometrial Transcriptome. Sci Rep, 10(1), pp. 6888. doi:10.1038/s41598-020-63798-8 (23 April 2020)
Kalavi K, Jorjani O, Faghihi MA, Mowla SJ. Cytokine Gene Expression Alterations in Human Macrophages Infected by Leishmania major. Cell J, 22(4), pp. 476-481. doi:10.22074/cellj.2021.6524 (22 April 2020)
Wang R, Tian B. APAlyzer: a bioinformatic package for analysis of alternative polyadenylation isoforms. Bioinformatics. doi:10.1093/bioinformatics/btaa266 (22 April 2020)
Bickler SW, Prieto JM, Cauvi DM, De Cos V, Nasamran C, Ameh E, Amin S, Nicholson S, Din H, Mocumbi AO, Noormahomed EV, Tellez-Isaias G, Fisch KM, De Maio A. Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco. Cell Stress Chaperones. doi:10.1007/s12192-020-01108-x (21 April 2020)
Wiebe DS, Omelyanchuk NA, Mukhin AM, Grosse I, Lashin SA, Zemlyanskaya EV, Mironova VV. Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. Genes (Basel), 11(4). doi:10.3390/genes11040434 (17 April 2020)
Das P, Roychowdhury A, Das S, Roychoudhury S, Tripathy S. sigFeature: Novel Significant Feature Selection Method for Classification of Gene Expression Data Using Support Vector Machine and t Statistic. Front Genet, 11, pp. 247. doi:10.3389/fgene.2020.00247 (3 April 2020)
Guttula PK, Monteiro PT, Gupta MK. A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells. Comput Methods Programs Biomed, 192, pp. 105473. doi:10.1016/j.cmpb.2020.105473 (20 March 2020)
Ciciani M, Cantore T, Lauria M. rScudo: an R package for classification of molecular profiles using rank-based signatures. Bioinformatics. doi:10.1093/bioinformatics/btaa296 (12 May 2019)

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