Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My NCBI Filters

Results by year

Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1996 1
2000 1
2003 7
2004 13
2005 19
2006 30
2007 44
2008 52
2009 62
2010 51
2011 70
2012 81
2013 109
2014 118
2015 151
2016 166
2017 131
2018 126
2019 180
2020 166
2021 174
2022 140
2023 56

Text availability

Article attribute

Article type

Publication date

Search Results

1,802 results

Results by year

Filters applied: . Clear all
Page 1
Transcriptomic data of bevacizumab-adapted colorectal adenocarcinoma cells HCT-116.
Cesare S, Tiziano L, Elena L, Alessandro RF, Luca V, Annarosa A. Cesare S, et al. Data Brief. 2023 Mar 17;48:109069. doi: 10.1016/j.dib.2023.109069. eCollection 2023 Jun. Data Brief. 2023. PMID: 37066085 Free PMC article.
Raw data were preprocessed, normalized, filtered, and subjected to a differential expression analysis using standard R/Bioconductor packages (i.e., limma, RankProd). As consequence of Bevacizumab adaptation, 166 differentially expressed genes (DEGs) emerged, most of them ( …
Raw data were preprocessed, normalized, filtered, and subjected to a differential expression analysis using standard R/Bioconductor p …
Transcriptomic analysis of benznidazole-resistant and susceptible Trypanosoma cruzi populations.
Lima DA, Gonçalves LO, Reis-Cunha JL, Guimarães PAS, Ruiz JC, Liarte DB, Murta SMF. Lima DA, et al. Parasit Vectors. 2023 May 22;16(1):167. doi: 10.1186/s13071-023-05775-4. Parasit Vectors. 2023. PMID: 37217925 Free PMC article.
METHODS: All complementary DNA (cDNA) libraries were constructed from the epimastigote forms of each line, sequenced and analysed using the Prinseq and Trimmomatic tools for the quality analysis, STAR as the aligner for mapping the reads against the reference genome (T. cruzi Dm2 …
METHODS: All complementary DNA (cDNA) libraries were constructed from the epimastigote forms of each line, sequenced and analysed using the …
BRGenomics for analyzing high resolution genomics data in R.
DeBerardine M. DeBerardine M. Bioinformatics. 2023 May 19:btad331. doi: 10.1093/bioinformatics/btad331. Online ahead of print. Bioinformatics. 2023. PMID: 37208173
SUMMARY: I present here the R/Bioconductor package BRGenomics, which provides fast and flexible methods for post-alignment processing and analysis of high resolution genomics data within an interactive R environment. ...AVAILABILITY AND IMPLEMENTATION: BRGenomics is an R p …
SUMMARY: I present here the R/Bioconductor package BRGenomics, which provides fast and flexible methods for post-alignment processing …
RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.
Ramos M, Morgan M, Geistlinger L, Carey VJ, Waldron L. Ramos M, et al. Bioinformatics. 2023 May 19:btad330. doi: 10.1093/bioinformatics/btad330. Online ahead of print. Bioinformatics. 2023. PMID: 37208161
Ragged data are not rectangular or matrix-like, presenting informatics challenges for downstream statistical analyses. We present the RaggedExperiment R/Bioconductor data structure for lossless representation of ragged genomic data, with associated reshaping tools for flex …
Ragged data are not rectangular or matrix-like, presenting informatics challenges for downstream statistical analyses. We present the Ragged …
NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles.
Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. Maqueda JJ, et al. Int J Mol Sci. 2023 May 18;24(10):8961. doi: 10.3390/ijms24108961. Int J Mol Sci. 2023. PMID: 37240307 Free PMC article.
We explored miRNA datasets from gastric tumors and normal adjacent tissues (NATs) from TCGA repository, as well as proprietary 3D-cultured GC cell lines and corresponding EVs, in order to identify differentially represented tRFs using MINTmap and R/Bioconductor packages. S …
We explored miRNA datasets from gastric tumors and normal adjacent tissues (NATs) from TCGA repository, as well as proprietary 3D-cultured G …
Bioinformatics and Raman spectroscopy-based identification of key pathways and genes enabling differentiation between acute myeloid leukemia and T cell acute lymphoblastic leukemia.
Liang H, Kong X, Cao Z, Wang H, Liu E, Sun F, Qi J, Zhang Q, Zhou Y. Liang H, et al. Front Immunol. 2023 May 17;14:1194353. doi: 10.3389/fimmu.2023.1194353. eCollection 2023. Front Immunol. 2023. PMID: 37266435 Free PMC article.
For these analyses, four Gene Expression Omnibus datasets (GSE13204, GSE51082, GSE89565, and GSE131184) pertaining to acute leukemia were downloaded, and differentially expressed genes (DEGs) were then identified through comparisons of AML and T-ALL patient samples using the R …
For these analyses, four Gene Expression Omnibus datasets (GSE13204, GSE51082, GSE89565, and GSE131184) pertaining to acute leukemia were do …
Integrative analysis of gene expression and DNA methylation to identify biomarkers of non-genital warts induced by low-risk human papillomaviruses infection.
Alghamdi MA, Al-Eitan LN, Tarkhan AH. Alghamdi MA, et al. Heliyon. 2023 May 7;9(5):e16101. doi: 10.1016/j.heliyon.2023.e16101. eCollection 2023 May. Heliyon. 2023. PMID: 37215908 Free PMC article.
Identification of the differentially expressed and differentially methylated genes was carried out using the RnBeads R package and the edgeR Bioconductor package. Next, functional annotation of the identified genes was obtained using the Database for Annotation, Visualizat …
Identification of the differentially expressed and differentially methylated genes was carried out using the RnBeads R package and the edgeR …
MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale.
Kohler D, Staniak M, Tsai TH, Huang T, Shulman N, Bernhardt OM, MacLean BX, Nesvizhskii AI, Reiter L, Sabido E, Choi M, Vitek O. Kohler D, et al. J Proteome Res. 2023 May 5;22(5):1466-1482. doi: 10.1021/acs.jproteome.2c00834. Epub 2023 Apr 5. J Proteome Res. 2023. PMID: 37018319
The MSstats R-Bioconductor family of packages is widely used for statistical analyses of quantitative bottom-up mass spectrometry-based proteomic experiments to detect differentially abundant proteins. ...
The MSstats R-Bioconductor family of packages is widely used for statistical analyses of quantitative bottom-up mass spectrometry-bas …
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.
Boniolo F, Hoffmann M, Roggendorf N, Tercan B, Baumbach J, Castro MAA, Robertson AG, Saur D, List M. Boniolo F, et al. Bioinformatics. 2023 May 4;39(5):btad276. doi: 10.1093/bioinformatics/btad276. Bioinformatics. 2023. PMID: 37084275 Free PMC article.
Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking. AVAILABILITY AND IMPLEMENTATION: https://bioconductor.org/packages/devel/bioc/html/SPONGE.html....
Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression infor …
matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling.
Davis ES, Mu W, Lee S, Dozmorov MG, Love MI, Phanstiel DH. Davis ES, et al. Bioinformatics. 2023 May 4;39(5):btad197. doi: 10.1093/bioinformatics/btad197. Bioinformatics. 2023. PMID: 37084270 Free PMC article.
RESULTS: To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient generation of matched null ranges from a set of background ranges within the Bioconductor framework. AVAILABILITY AND IMPLEMENTATION: Pac …
RESULTS: To address this, we developed matchRanges, a propensity score-based covariate matching method for the efficient and convenient gene …
1,802 results

Searches related to "bioconductor"