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Irizarry R, et al. (2015) Biomedical Data Science. Course Notes, EdX PH525.1x.
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). PMC4509590
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, and Smyth, GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucl. Acids Res; doi:10.1093/nar/gkv007
Love M, Huber W, and Anders S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550; doi:10.1186/s13059-014-0550-8
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

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2015-08-29T17:30:08-04:00.

Camargo RD, Herai RH, Santos LN, Bento FM, Lima JE, Marques-Souza H, Figueira A. De novo transcriptome assembly and analysis to identify potential gene targets for RNAi-mediated control of the tomato leafminer (Tuta absoluta) BMC Genomics, 16(1), pp. 635. doi:10.1186/s12864-015-1841-5 (26 August 2015)
Bennett M, Evans KE, Yu S, Teng Y, Webster RM, Powell J, Waters R, Reed SH. Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure Sci Rep, 5, pp. 13395. doi:10.1038/srep13395 (26 August 2015)
Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, Kutmon M, Jaillard M, Evelo CT. Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment BMC Bioinformatics, 16(1), pp. 267. doi:10.1186/s12859-015-0708-8 (23 August 2015)
Everson TM, Lyons G, Zhang H, Soto-Ramírez N, Lockett GA, Patil VK, Merid SK, Sӧderhӓll C, Melén E, Holloway JW, Arshad SH, Karmaus W. DNA methylation loci associated with atopy and high serum IgE: a genome-wide application of recursive Random Forest feature selection Genome Med, 7(1), pp. 89. doi:10.1186/s13073-015-0213-8 (21 August 2015)
Castiglioni L, Colazzo F, Fontana L, Colombo GI, Piacentini L, Bono E, Milano G, Paleari S, Palermo A, Guerrini U, Tremoli E, Sironi L. Evaluation of Left Ventricle Function by Regional Fractional Area Change (RFAC) in a Mouse Model of Myocardial Infarction Secondary to Valsartan Treatment PLoS One, 10(8), pp. e0135778. doi:10.1371/journal.pone.0135778 (20 August 2015)
Vincent KM, Findlay SD, Postovit LM. Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles Breast Cancer Res, 17(1), pp. 114. doi:10.1186/s13058-015-0613-0 (20 August 2015)
Pacholewska A, Jagannathan V, Drögemüller M, Klukowska-Rötzler J, Lanz S, Hamza E, Dermitzakis ET, Marti E, Leeb T, Gerber V. Impaired Cell Cycle Regulation in a Natural Equine Model of Asthma PLoS One, 10(8), pp. e0136103. doi:10.1371/journal.pone.0136103 (20 August 2015)
Lun AT, Smyth GK. diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. BMC Bioinformatics, 16(1), pp. 258. doi:10.1186/s12859-015-0683-0 (19 August 2015)
Nezami Ranjbar MR, Poto CD, Wang Y, Ressom HW. SIMAT: GC-SIM-MS data analysis tool. BMC Bioinformatics, 16(1), pp. 259. doi:10.1186/s12859-015-0681-2 (19 August 2015)
Jacob L, Gagnon-Bartsch JA, Speed TP. Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed. Biostatistics. doi:10.1093/biostatistics/kxv026 (17 August 2015)
Hsiao C, Liu M, Stanton R, McGee M, Qian Y, Scheuermann RH. Mapping cell populations in flow cytometry data for cross-sample comparison using the Friedman-Rafsky test statistic as a distance measure. Cytometry A. doi:10.1002/cyto.a.22735 (14 August 2015)
Coetzee SG, Coetzee GA, Hazelett DJ. motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformatics. doi:10.1093/bioinformatics/btv470 (12 August 2015)
Stacchiotti S, Pantaleo MA, Negri T, Astolfi A, Tazzari M, Dagrada GP, Urbini M, Indio V, Maestro R, Gronchi A, Fiore M, Dei Tos AP, Conca E, Palassini E, Vincenzi B, Grosso F, Pilotti S, Castelli C, Casali PG. Efficacy and biological activity of imatinib in metastatic dermatifibrosarcoma protuberans (DFSP). Clin Cancer Res. doi:10.1158/1078-0432.CCR-15-1243 (10 August 2015)
Gust KA, Nanduri B, Rawat A, Wilbanks MS, Ang CY, Johnson DR, Pendarvis K, Chen X, Quinn MJ Jr, Johnson MS, Burgess SC, Perkins EJ. Systems toxicology identifies mechanistic impacts of 2-amino-4,6-dinitrotoluene (2A-DNT) exposure in Northern Bobwhite BMC Genomics, 16(1), pp. 587. doi:10.1186/s12864-015-1798-4 (7 August 2015)
Zhang YC, Zhang SW, Liu L, Liu H, Zhang L, Cui X, Huang Y, Meng J. Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model Biomed Res Int, 2015, pp. 852070. doi:10.1155/2015/852070 (2 August 2015)
Alentorn A, Durán-Peña A, Malousi A, Marie Y, Mokhtari K, Sanson M, Hoang-Xuan K, Delattre JY, Idbaih A, Vecht C. Differential gene methylation in paired glioblastomas suggests a role of immune response pathways in tumor progression. J Neurooncol. doi:10.1007/s11060-015-1869-z (30 July 2015)
Stephan-Otto Attolini C, Peña V, Rossell D. Designing alternative splicing RNA-seq studies. Beyond generic guidelines. Bioinformatics. doi:10.1093/bioinformatics/btv436 (27 July 2015)
Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely KN. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. doi:10.1093/nar/gkv715 (15 July 2015)
Gehring JS, Fischer B, Lawrence M, Huber W. SomaticSignatures: inferring mutational signatures from single-nucleotide variants. Bioinformatics. doi:10.1093/bioinformatics/btv408 (10 July 2015)
Wang Y, Qian CY, Li XP, Zhang Y, He H, Wang J, Chen J, Cui JJ, Liu R, Zhou H, Xiao L, Xu XJ, Zheng Y, Fu YL, Chen ZY, Chen X, Zhang W, Ye CC, Zhou HH, Yin JY, Liu ZQ. Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer. Sci Rep, 5, pp. 11671. doi:10.1038/srep11671 (10 July 2015)

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