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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 2022-12-07T23:30:07-05:00.

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)

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)

Hoberecht L, Perampalam P, Lun A, Fortin JP. A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies. Nat Commun, 13(1), pp. 6568. doi:10.1038/s41467-022-34320-7 (2 November 2022)

Wu JX, Pascovici D, Wu Y, Walker AK, Mirzaei M. Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data. Methods Mol Biol, 2426, pp. 375-390. doi:10.1007/978-1-0716-1967-4_17 (30 October 2022)

Gregori J, Sánchez À, Villanueva J. msmsEDA & msmsTests: Label-Free Differential Expression by Spectral Counts. Methods Mol Biol, 2426, pp. 197-242. doi:10.1007/978-1-0716-1967-4_10 (30 October 2022)

Wang Q, Li M, Wu T, Zhan L, Li L, Chen M, Xie W, Xie Z, Hu E, Xu S, Yu G. Exploring Epigenomic Datasets by ChIPseeker. Curr Protoc, 2(10), pp. e585. doi:10.1002/cpz1.585 (27 October 2022)

Gurumurthy RK, Pleissner KP, Chumduri C, Meyer TF, Mäurer AP. Single object profiles regression analysis (SOPRA): a novel method for analyzing high-content cell-based screens. BMC Bioinformatics, 23(1), pp. 440. doi:10.1186/s12859-022-04981-8 (21 October 2022)

Guo Z, Shafik AM, Jin P, Wu H. Differential RNA methylation analysis for MeRIP-seq data under general experimental design. Bioinformatics, 38(20), pp. 4705-4712. doi:10.1093/bioinformatics/btac601 (14 October 2022)

Naik P, Joseph J. Temporal Transcriptome Analysis Suggests Modulation of Key Pathways and Hub Genes in a Mice Model of Multi-Drug Resistant (MDR) Pseudomonas aeruginosa Endophthalmitis. Curr Eye Res, 47(11), pp. 1559-1566. doi:10.1080/02713683.2022.2124276 (2 October 2022)

Zhang M, Liu J, Zhang X, Zhang S, Jiang Y, Yu Z, Xie T, Chen Y, Chen L, Li J. Mechanism of Yangxin Tongmai Decoction in the Treatment of Coronary Heart Disease with Blood Stasis Syndrome Based on Network Pharmacology and Molecular Docking. Evid Based Complement Alternat Med, 2022, pp. 4692217. doi:10.1155/2022/4692217 (30 September 2022)

Herrera M, Keynan Y, McLaren PJ, Isaza JP, Abrenica B, López L, Marin D, Rueda ZV. Gene expression profiling identifies candidate biomarkers for new latent tuberculosis infections. A cohort study. PLoS One, 17(9), pp. e0274257. doi:10.1371/journal.pone.0274257 (28 September 2022)

Li D, Zand MS, Dye TD, Goniewicz ML, Rahman I, Xie Z. An evaluation of RNA-seq differential analysis methods. PLoS One, 17(9), pp. e0264246. doi:10.1371/journal.pone.0264246 (16 September 2022)

Ferrer-Bonsoms JA, Gimeno M, Olaverri D, Sacristan P, Lobato C, Castilla C, Carazo F, Rubio A. EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains. NAR Genom Bioinform, 4(3), pp. lqac067. doi:10.1093/nargab/lqac067 (15 September 2022)

Gründing AR, Schneider MA, Richtmann S, Kriegsmann M, Winter H, Martinez-Delgado B, Varona S, Liu B, DeLuca DS, Held J, Wrenger S, Muley T, Meister M, Welte T, Janciauskiene S. Lung Adenocarcinoma Cell Sensitivity to Chemotherapies: A Spotlight on Lipid Droplets and SREBF1 Gene. Cancers (Basel), 14(18). doi:10.3390/cancers14184454 (14 September 2022)

Visentin L, Scarpellino G, Chinigò G, Munaron L, Ruffinatti FA. BioTEA: Containerized Methods of Analysis for Microarray-Based Transcriptomics Data. Biology (Basel), 11(9). doi:10.3390/biology11091346 (13 September 2022)

Li H, Jia X, Bai YQ, Wu P, Guo HL, Yun KM, Gao CR, Guo XJ. Gene Expression Profiles at Different Time Points after Acute Myocardial Infarction in Mice. Fa Yi Xue Za Zhi, 38(3), pp. 343-349. doi:10.12116/j.issn.1004-5619.2021.410505 (25 June 2022)