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Ramos, M, et al. (2017) Software for the Integration of Multiomics Experiments in Bioconductor Cancer Research 77:e39-e42. doi:10.1158/0008-5472.CAN-17-0344

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 2019-03-25T18:00:10-04:00.

Gorrie-Stone TJ, Smart MC, Saffari A, Malki K, Hannon E, Burrage J, Mill J, Kumari M, Schalkwyk LC. Bigmelon: tools for analysing large DNA methylation datasets. Bioinformatics, 35(6), pp. 981-986. doi:10.1093/bioinformatics/bty713 (15 March 2019)

Robertson DS, Wildenhain J, Javanmard A, Karp NA. onlineFDR: an R package to control the false discovery rate for growing data repositories. Bioinformatics. doi:10.1093/bioinformatics/btz191 (14 March 2019)

Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C. RnBeads 2.0: comprehensive analysis of DNA methylation data. Genome Biol, 20(1), pp. 55. doi:10.1186/s13059-019-1664-9 (14 March 2019)

Su W, Sun J, Shimizu K, Kadota K. TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data. BMC Res Notes, 12(1), pp. 133. doi:10.1186/s13104-019-4179-2 (13 March 2019)

Pećina-Šlaus N, Kafka A, Gotovac Jerčić K, Logara M, Bukovac A, Bakarić R, Borovečki F. Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades. Int J Mol Sci, 20(5). doi:10.3390/ijms20051251 (12 March 2019)

Myint L, Avramopoulos DG, Goff LA, Hansen KD. Linear models enable powerful differential activity analysis in massively parallel reporter assays. BMC Genomics, 20(1), pp. 209. doi:10.1186/s12864-019-5556-x (12 March 2019)

Stamm K, Tomita-Mitchell A, Bozdag S. GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display. BMC Bioinformatics, 20(1), pp. 115. doi:10.1186/s12859-019-2697-5 (6 March 2019)

Schmich F, Kuipers J, Merdes G, Beerenwinkel N. netprioR: a probabilistic model for integrative hit prioritisation of genetic screens. Stat Appl Genet Mol Biol. doi:10.1515/sagmb-2018-0033 (6 March 2019)

Mounir M, Lucchetta M, Silva TC, Olsen C, Bontempi G, Chen X, Noushmehr H, Colaprico A, Papaleo E. New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx. PLoS Comput Biol, 15(3), pp. e1006701. doi:10.1371/journal.pcbi.1006701 (5 March 2019)

Campos-Laborie FJ, Risueño A, Ortiz-Estévez M, Rosón-Burgo B, Droste C, Fontanillo C, Loos R, Sánchez-Santos JM, Trotter MW, De Las Rivas J. DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling. Bioinformatics. doi:10.1093/bioinformatics/btz148 (1 March 2019)

Olson ND, Shah N, Kancherla J, Wagner J, Paulson JN, Corrada-Bravo H. metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data. Bioinformatics. doi:10.1093/bioinformatics/btz136 (1 March 2019)

Guo L, Lv J, Huang YF, Hao DJ, Liu JJ. Bioinformatics analyses of differentially expressed genes associated with spinal cord injury: A microarray-based analysis in a mouse model. Neural Regen Res, 14(7), pp. 1262-1270. doi:10.4103/1673-5374.251335 (26 February 2019)

Liao Y, Smyth GK, Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. doi:10.1093/nar/gkz114 (20 February 2019)

Kim B, Lee E, Kim JK. Analysis of Technical and Biological Variability in Single-Cell RNA Sequencing. Methods Mol Biol, 1935, pp. 25-43. doi:10.1007/978-1-4939-9057-3_3 (14 February 2019)

Bacher R. Normalization for Single-Cell RNA-Seq Data Analysis. Methods Mol Biol, 1935, pp. 11-23. doi:10.1007/978-1-4939-9057-3_2 (14 February 2019)

Ashtiani M, Nickchi P, Jahangiri-Tazehkand S, Safari A, Mirzaie M, Jafari M. IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis. BMC Bioinformatics, 20(1), pp. 73. doi:10.1186/s12859-019-2659-y (12 February 2019)

Martorell-Marugán J, González-Rumayor V, Carmona-Sáez P. mCSEA: Detecting subtle differentially methylated regions. Bioinformatics. doi:10.1093/bioinformatics/btz096 (12 February 2019)

Cortés-Pereira E, Fernández-Tajes J, Fernández-Moreno M, Vázquez-Mosquera ME, Relaño S, Ramos-Louro P, Durán-Sotuela A, Dalmao-Fernández A, Oreiro N, Blanco FJ, Rego-Pérez I. Mitochondrial DNA (mtDNA) haplogroups J and H are differentially associated with the methylation status of articular cartilage: potential role in apoptosis and metabolic and developmental processes. Arthritis Rheumatol. doi:10.1002/art.40857 (12 February 2019)

Jeitziner R, Carrière M, Rougemont J, Oudot S, Hess K, Brisken C. Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis. Bioinformatics. doi:10.1093/bioinformatics/btz052 (7 February 2019)

Gopaulakrishnan S, Pollack S, Stubbs BJ, Pagès H, Readey J, Davis S, Waldron L, Morgan M, Carey V. restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. F1000Res, 8, pp. 21. doi:10.12688/f1000research.17518.1 (7 January 2019)