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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 2023-08-11T10:56:17+00:00.
Klein HU. demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models.
Bioinformatics, 39(8).
doi:10.1093/bioinformatics/btad481 (1 August 2023)
Feng H, Meng G, Lin T, Parikh H, Pan Y, Li Z, Krischer J, Li Q. ISLET: individual-specific reference panel recovery improves cell-type-specific inference.
Genome Biol, 24(1), pp. 174.
doi:10.1186/s13059-023-03014-8 (26 July 2023)
Huang T, Staniak M, Veiga Leprevost FD, Figueroa-Navedo AM, Ivanov AR, Nesvizhskii AI, Choi M, Vitek O. Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling.
J Proteome Res, 22(8), pp. 2641-2659.
doi:10.1021/acs.jproteome.3c00155 (19 July 2023)
Weber LM, Saha A, Datta A, Hansen KD, Hicks SC. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes.
Nat Commun, 14(1), pp. 4059.
doi:10.1038/s41467-023-39748-z (10 July 2023)
Ruiz-Arenas C, Abarrategui L, Hernandez-Ferrer C, Escribà-Montagut X, Pelegrí-Sisó D, Ryser-Welch P, Vrijheid M, Bustamante M, Grazuleviciene R, Lepeule J, Mathai M, Vafeiadi M, Beltran S, Pérez-Jurado LA, González JR. Epimutation detection in the clinical context: guidelines and a use case from a new Bioconductor package.
Epigenetics, 18(1), pp. 2230670.
doi:10.1080/15592294.2023.2230670 (6 July 2023)
Liao Y, Raghu D, Pal B, Mielke LA, Shi W. cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data.
Bioinformatics, 39(7).
doi:10.1093/bioinformatics/btad439 (1 July 2023)
Song GY, Guo XN, Yao J, Lu ZN, Xie JH, Wu F, He J, Fu ZL, Han J. Differential expression profiles and functional analysis of long non-coding RNAs in calcific aortic valve disease.
BMC Cardiovasc Disord, 23(1), pp. 326.
doi:10.1186/s12872-023-03311-x (27 June 2023)
Hernández HG, Aranzazu-Moya GC, Pinzón-Reyes EH. Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers.
Biomedicines, 11(7).
doi:10.3390/biomedicines11071797 (23 June 2023)
Dehghani K, Stanek A, Bagherabadi A, Atashi F, Beygi M, Hooshmand A, Hamedi P, Farhang M, Bagheri S, Zolghadri S. CCND1 Overexpression in Idiopathic Dilated Cardiomyopathy: A Promising Biomarker?
Genes (Basel), 14(6).
doi:10.3390/genes14061243 (10 June 2023)
Singh R, He X, Park AK, Hardison RC, Zhu X, Li Q. RETROFIT: REFERENCE-FREE DECONVOLUTION OF CELL-TYPE MIXTURES IN SPATIAL TRANSCRIPTOMICS.
bioRxiv.
doi:10.1101/2023.06.07.544126 (9 June 2023)
Jalili V, Cremona MA, Palluzzi F. Rescuing biologically relevant consensus regions across replicated samples.
BMC Bioinformatics, 24(1), pp. 240.
doi:10.1186/s12859-023-05340-x (7 June 2023)
DeBerardine M. BRGenomics for analyzing high-resolution genomics data in R.
Bioinformatics, 39(6).
doi:10.1093/bioinformatics/btad331 (1 June 2023)
Ramos M, Morgan M, Geistlinger L, Carey VJ, Waldron L. RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.
Bioinformatics, 39(6).
doi:10.1093/bioinformatics/btad330 (1 June 2023)
Meyer L, Eling N, Bodenmiller B. cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data.
bioRxiv.
doi:10.1101/2023.05.24.542115 (24 May 2023)
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)
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)
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)
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)
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