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Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 1:kxab030. doi: 10.1093/biostatistics/kxab030. Epub ahead of print. PMID: 34467372.
Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun. 2022 Jun 27;13(1):3695. doi: 10.1038/s41467-022-31411-3. PMID: 35760813; PMCID: PMC9237024
Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O'Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022 Jan 12;2(1):100085. doi: 10.1016/j.xgen.2021.100085. Epub 2022 Jan 13. PMID: 35199087; PMCID: PMC8863334
He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11. PMID: 35277707; PMCID: PMC8933848

Recent

20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2022-12-09T00:00:07-05:00.

Matteo C, Chiara R, Davide R, Nicola V. benchdamic: benchmarking of differential abundance methods for microbiome data. Bioinformatics. doi:10.1093/bioinformatics/btac778 (7 December 2022)
Kameda-Smith MM, Zhu H, Luo EC, Suk Y, Xella A, Yee B, Chokshi C, Xing S, Tan F, Fox RG, Adile AA, Bakhshinyan D, Brown K, Gwynne WD, Subapanditha M, Miletic P, Picard D, Burns I, Moffat J, Paruch K, Fleming A, Hope K, Provias JP, Remke M, Lu Y, Reya T, Venugopal C, Reimand J, Wechsler-Reya RJ, Yeo GW, Singh SK. Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma Nat Commun, 13, pp. 7506. doi:10.1038/s41467-022-35118-3 (6 December 2022)
Deng J, Lin J, Liu C, Li J, Cai J, Zhou X, Li X. N7-methylguanosine methylation-related regulator genes as biological markers in predicting prognosis for melanoma Sci Rep, 12, pp. 21082. doi:10.1038/s41598-022-25698-x (6 December 2022)
Alharthi J, Bayoumi A, Thabet K, Pan Z, Gloss BS, Latchoumanin O, Lundberg M, Twine NA, McLeod D, Alenizi S, Adams LA, Weltman M, Berg T, Liddle C, George J, Eslam M. A metabolic associated fatty liver disease risk variant in MBOAT7 regulates toll like receptor induced outcomes Nat Commun, 13, pp. 7430. doi:10.1038/s41467-022-35158-9 (6 December 2022)
Yi M, Wu Y, Niu M, Zhu S, Zhang J, Yan Y, Zhou P, Dai Z, Wu K. Anti-TGF-β/PD-L1 bispecific antibody promotes T cell infiltration and exhibits enhanced antitumor activity in triple-negative breast cancer J Immunother Cancer, 10(12), pp. e005543. doi:10.1136/jitc-2022-005543 (2 December 2022)
Schloesser D, Lindenthal L, Sauer J, Chung KJ, Chavakis T, Griesser E, Baskaran P, Maier-Habelsberger U, Fundel-Clemens K, Schlotthauer I, Watson CK, Swee LK, Igney F, Park JE, Huber-Lang MS, Thomas MJ, El Kasmi KC, Murray PJ. Senescent cells suppress macrophage-mediated corpse removal via upregulation of the CD47-QPCT/L axis J Cell Biol, 222(2), pp. e202207097. doi:10.1083/jcb.202207097 (2 December 2022)
Vo Ngoc LDT, Osei R, Dohr K, Olsen C, Seneca S, Gheldof A. EDIR: Exome Database of Interspersed Repeats. Bioinformatics. doi:10.1093/bioinformatics/btac771 (1 December 2022)
Jeanmougin M, Brodal HP, Dietrichson Pharo H, Vedeld HM, Lind GE. PoDCall: positive droplet calling and normalisation of droplet digital PCR DNA methylation data. Bioinformatics. doi:10.1093/bioinformatics/btac766 (30 November 2022)
Class CA, Lukan CJ, Bristow CA, Do KA. Easy NanoString nCounter data analysis with the NanoTube. Bioinformatics. doi:10.1093/bioinformatics/btac762 (28 November 2022)
Mu D, Wu X, Feijó A, Wu W, Wen Z, Cheng J, Xia L, Yang Q, Shan W, Ge D. Transcriptome analysis of pika heart tissue reveals mechanisms underlying the adaptation of a keystone species on the roof of the world Front Genet, 13, pp. 1020789. doi:10.3389/fgene.2022.1020789 (23 November 2022)
Bilbao-Arribas M, Jugo BM. Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep Front Genet, 13, pp. 1067350. doi:10.3389/fgene.2022.1067350 (22 November 2022)
Zhang Y, Li Q, Wang C, Liu S. Transcriptomic and metabolomic analyses reveal the antifungal mechanism of the compound phenazine-1-carboxamide on Rhizoctonia solani AG1IA Front Plant Sci, 13, pp. 1041733. doi:10.3389/fpls.2022.1041733 (22 November 2022)
Yang J, Zhang L, Li Y, Chen M. Identifying key m6A-methylated lncRNAs and genes associated with neural tube defects via integrative MeRIP and RNA sequencing analyses Front Genet, 13, pp. 974357. doi:10.3389/fgene.2022.974357 (22 November 2022)
Naik S, Mohammed A. Coexpression network analysis of human candida infection reveals key modules and hub genes responsible for host-pathogen interactions Front Genet, 13, pp. 917636. doi:10.3389/fgene.2022.917636 (22 November 2022)
Long W, Huang G, Yao X, Lv L, Yu C, Wang K. Untargeted metabolism approach reveals difference of varieties of bud and relation among characteristics of grafting seedlings in Camellia oleifera Front Plant Sci, 13, pp. 1024353. doi:10.3389/fpls.2022.1024353 (21 November 2022)
Singh A, Ambaru B, Bandsode V, Ahmed N. Panomics to decode virulence and fitness in Gram-negative bacteria Front Cell Infect Microbiol, 12, pp. 1061596. doi:10.3389/fcimb.2022.1061596 (21 November 2022)
Petkov S, Herrera C, Else L, Lebina L, Opoka D, Seiphetlo TB, Pillay AD, Mugaba S, Namubiru P, Odoch G, Ssemata AS, Serwanga J, Kaleebu P, Webb EL, Khoo S, Martinson N, Gray CM, Fox J, Chiodi F. Short-term oral pre-exposure prophylaxis against HIV-1 modulates the transcriptome of foreskin tissue in young men in Africa Front Immunol, 13, pp. 1009978. doi:10.3389/fimmu.2022.1009978 (18 November 2022)
Gu Z, Hübschmann D. rGREAT: an R/Bioconductor package for functional enrichment on genomic regions. Bioinformatics. doi:10.1093/bioinformatics/btac745 (17 November 2022)
Lee DY, Hah JH, Jeong WJ, Chung EJ, Kwon TK, Ahn SH, Sung MW, Kwon SK. The Expression of Defensin-Associated Genes May Be Correlated With Lymph Node Metastasis of Early-Stage Tongue Cancer. Clin Exp Otorhinolaryngol, 15(4), pp. 372-379. doi:10.21053/ceo.2022.00150 (16 November 2022)
Liou L, Hornburg M, Robertson DS. Global FDR control across multiple RNAseq experiments. Bioinformatics. doi:10.1093/bioinformatics/btac718 (3 November 2022)

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