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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


20 most recent PubMed and PubMed Central citations mentioning "Bioconductor". For a complete list, go to PubMed and PubMed Central. Last updated 2023-06-04T23:00:08-04:00.

Lima DA, Gonçalves LO, Reis-Cunha JL, Guimarães PAS, Ruiz JC, Liarte DB, Murta SMF. Transcriptomic analysis of benznidazole-resistant and susceptible Trypanosoma cruzi populations. Parasit Vectors, 16(1), pp. 167. doi:10.1186/s13071-023-05775-4 (22 May 2023)
DeBerardine M. BRGenomics for analyzing high resolution genomics data in R. Bioinformatics. doi:10.1093/bioinformatics/btad331 (19 May 2023)
Ramos M, Morgan M, Geistlinger L, Carey VJ, Waldron L. RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor. Bioinformatics. doi:10.1093/bioinformatics/btad330 (19 May 2023)
Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles. Int J Mol Sci, 24(10). doi:10.3390/ijms24108961 (18 May 2023)
Liang H, Kong X, Cao Z, Wang H, Liu E, Sun F, Qi J, Zhang Q, Zhou Y. Bioinformatics and Raman spectroscopy-based identification of key pathways and genes enabling differentiation between acute myeloid leukemia and T cell acute lymphoblastic leukemia. Front Immunol, 14, pp. 1194353. doi:10.3389/fimmu.2023.1194353 (17 May 2023)
Alghamdi MA, Al-Eitan LN, Tarkhan AH. Integrative analysis of gene expression and DNA methylation to identify biomarkers of non-genital warts induced by low-risk human papillomaviruses infection. Heliyon, 9(5), pp. e16101. doi:10.1016/j.heliyon.2023.e16101 (7 May 2023)
Boniolo F, Hoffmann M, Roggendorf N, Tercan B, Baumbach J, Castro MAA, Robertson AG, Saur D, List M. spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinformatics, 39(5). doi:10.1093/bioinformatics/btad276 (4 May 2023)
Davis ES, Mu W, Lee S, Dozmorov MG, Love MI, Phanstiel DH. matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling. Bioinformatics, 39(5). doi:10.1093/bioinformatics/btad197 (4 May 2023)
Olbrich M, Künstner A, Busch H. MBECS: Microbiome Batch Effects Correction Suite. BMC Bioinformatics, 24(1), pp. 182. doi:10.1186/s12859-023-05252-w (3 May 2023)
Zhao Q, Wang P, Zhao M, Hong J, Zhang N, Lin K, Li Y. Study on the pharmacological mechanisms of sodium-glucose co-transporter 2 inhibitors in obesity-related atrial fibrillation based on network pharmacology and experimental verification. Ann Transl Med, 11(8), pp. 300. doi:10.21037/atm-23-1321 (30 April 2023)
Kambey PA, Liu WY, Wu J, Tang C, Buberwa W, Saro A, Nyalali AMK, Gao D. Amphiregulin blockade decreases the levodopa-induced dyskinesia in a 6-hydroxydopamine Parkinson's disease mouse model. CNS Neurosci Ther. doi:10.1111/cns.14229 (26 April 2023)
Haldar A, Oza VH, DeVoss NS, Clark AD, Lasseigne BN. CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis. bioRxiv. doi:10.1101/2023.04.21.537877 (25 April 2023)
Hediyeh-Zadeh S, Webb AI, Davis MJ. MsImpute: Estimation of missing peptide intensity data in label-free quantitative mass spectrometry. Mol Cell Proteomics, pp. 100558. doi:10.1016/j.mcpro.2023.100558 (25 April 2023)
Liu W, Chen W, Hu M, Wang G, Hu Y, He Q, Xu Y, Tan J, Wang H, Huo L. Bioinformatics analysis combined with molecular dynamics simulation validation to elucidate the potential molecular mechanisms of Jianshen Decoction for treatment of osteoporotic fracture. Medicine (Baltimore), 102(16), pp. e33610. doi:10.1097/MD.0000000000033610 (21 April 2023)
Sayols S. rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. MicroPubl Biol, 2023. doi:10.17912/micropub.biology.000811 (18 April 2023)
Poudel SK, Padmanabhan R, Dave H, Guinta K, Stevens T, Sanaka MR, Chahal P, Sohal DPS, Khorana AA, Eng C. Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease. PLoS One, 18(4), pp. e0283021. doi:10.1371/journal.pone.0283021 (18 April 2023)
Choi S, Schilder BM, Abbasova L, Murphy AE, Skene NG. EpiCompare: R package for the comparison and quality control of epigenomic peak files. Bioinform Adv, 3(1), pp. vbad049. doi:10.1093/bioadv/vbad049 (13 April 2023)
Yu R, Wang Y, Liang Q, Xu Y, Yusf AE, Sun L. Identification of potential biomarkers and pathways for sepsis using RNA sequencing technology and bioinformatic analysis. Heliyon, 9(4), pp. e15034. doi:10.1016/j.heliyon.2023.e15034 (3 April 2023)
Sciacca E, Alaimo S, Silluzio G, Ferro A, Latora V, Pitzalis C, Pulvirenti A, Lewis MJ. DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data. Bioinformatics, 39(4). doi:10.1093/bioinformatics/btad192 (3 April 2023)
Ogata JD, Mu W, Davis ES, Xue B, Harrell JC, Sheffield NC, Phanstiel DH, Love MI, Dozmorov MG. excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. Bioinformatics, 39(4). doi:10.1093/bioinformatics/btad198 (3 April 2023)


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