Publications

Bioconductor F1000 Research Channel launched!

Featured

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 2021-02-24T15:00:11-05:00.

Pirkl M, Beerenwinkel N. Inferring perturbation profiles of cancer samples. Bioinformatics. doi:10.1093/bioinformatics/btab113 (22 February 2021)
Want MY, Tsuji T, Singh PK, Thorne JL, Matsuzaki J, Karasik E, Gillard B, Cortes Gomez E, Koya RC, Lugade A, Odunsi K, Battaglia S. WHSC1/NSD2 regulates immune infiltration in prostate cancer. J Immunother Cancer, 9(2). doi:10.1136/jitc-2020-001374 (17 February 2021)
Chao KH, Barton K, Palmer S, Lanfear R. sangeranalyseR: simple and Interactive Processing of Sanger Sequencing Data in R. Genome Biol Evol. doi:10.1093/gbe/evab028 (16 February 2021)
Danková Z, Grendár M, Dvorská D, Braný D, Stastny I, Bobrovská M, Balhárek T, Zubor P. miRNA profile of luminal breast cancer subtyptes in Slovak women. Ceska Gynekol, 85(3), pp. 174-180. doi: (11 February 2021)
Borges H, Hesse AM, Kraut A, Couté Y, Brun V, Burger T. Well Plate Maker: A user-friendly randomized block design application to limit batch effects in largescale biomedical studies. Bioinformatics. doi:10.1093/bioinformatics/btab065 (4 February 2021)
Lian Y, Wang Q, Mu J, Liu H, Xu T, Fan S, Tang F, Feng T, Xu W, Jin N, Cheng F, Wang X. Network pharmacology assessment of Qingkailing injection treatment of cholestatic hepatitis. J Tradit Chin Med, 41(1), pp. 167-180. doi:10.19852/j.cnki.jtcm.20201208.001 (2 February 2021)
Hettegger P, Vierlinger K, Weinhaeusel A. Random rotation for identifying differentially expressed genes with linear models following batch effect correction. Bioinformatics. doi:10.1093/bioinformatics/btab063 (1 February 2021)
Mehmood A, Laiho A, Elo LL. Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies. RNA Biol, pp. 1-8. doi:10.1080/15476286.2020.1868151 (30 January 2021)
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)
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)
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)
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)

Books

Monograph     R Programming for Bioinformatics     Bioconductor Case Studies

Book Chapters

Technical Reports and Working Papers

Compendia

Literature Search »

 

Courses & Conferences »

Bioconductor courses and conferences explore R programming and the analysis of genomic data. View catalog of a recent course material.

Packages »

Bioconductor's stable, semi-annual release:

Bioconductor is also available via Docker and Amazon Machine Images.