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 173
2022 142
2023 110
2024 36

Text availability

Article attribute

Article type

Publication date

Search Results

1,892 results

Results by year

Filters applied: . Clear all
Page 1
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.
Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib WA, Heo L, Laird PW, Berman BP, Triche TJ Jr, Shen H. Zhou W, et al. Nucleic Acids Res. 2024 Apr 12;52(6):e32. doi: 10.1093/nar/gkae097. Nucleic Acids Res. 2024. PMID: 38412294 Free PMC article.
We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. ...
We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, fo …
NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders.
Ruiz-Arenas C, Marín-Goñi I, Wang L, Ochoa I, Pérez-Jurado LA, Hernaez M. Ruiz-Arenas C, et al. Nucleic Acids Res. 2024 Apr 10:gkae197. doi: 10.1093/nar/gkae197. Online ahead of print. Nucleic Acids Res. 2024. PMID: 38597610
When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a classical enrichment analysis identified gene sets irrelevant to the phenotype. NetActivity is publicly available in Bioconductor and …
When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a c …
lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression.
Maden SK, Huuki-Myers LA, Kwon SH, Collado-Torres L, Maynard KR, Hicks SC. Maden SK, et al. bioRxiv [Preprint]. 2024 Apr 6:2024.04.04.588105. doi: 10.1101/2024.04.04.588105. bioRxiv. 2024. PMID: 38617294 Free PMC article. Preprint.
Using simulated and real datasets, we demonstrate how lute adjusts for differences in cell sizes to improve the accuracy of cell composition. Software is available from https://bioconductor.org/packages/lute....
Using simulated and real datasets, we demonstrate how lute adjusts for differences in cell sizes to improve the accuracy of cell composition …
Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2).
Lewinski M, Brüggemann M, Köster T, Reichel M, Bergelt T, Meyer K, König J, Zarnack K, Staiger D. Lewinski M, et al. Nat Protoc. 2024 Apr;19(4):1183-1234. doi: 10.1038/s41596-023-00935-3. Epub 2024 Jan 26. Nat Protoc. 2024. PMID: 38278964 Review.
Finally, we describe a bioinformatics workflow to determine targets of Arabidopsis RBPs from iCLIP data, covering all steps from downloading sequencing reads to identifying cross-linking events ( https://github.com/malewins/Plant-iCLIPseq ), and present the R/Bioconductor …
Finally, we describe a bioinformatics workflow to determine targets of Arabidopsis RBPs from iCLIP data, covering all steps from downloading …
Regional analysis to delineate intrasample heterogeneity with RegionalST.
Lyu Y, Wu C, Sun W, Li Z. Lyu Y, et al. Bioinformatics. 2024 Mar 29;40(4):btae186. doi: 10.1093/bioinformatics/btae186. Bioinformatics. 2024. PMID: 38579257 Free PMC article.
AVAILABILITY AND IMPLEMENTATION: The implementation of our method is available as an open-source R/Bioconductor package with a user-friendly manual available at https://bioconductor.org/packages/release/bioc/html/RegionalST.html....
AVAILABILITY AND IMPLEMENTATION: The implementation of our method is available as an open-source R/Bioconductor package with a user-f …
Immunomodulatory Effect of Phytoactive Compounds on Human Health: A Narrative Review Integrated with Bioinformatics Approach.
Choudhary S, Khan S, Rustagi S, Rajpal VR, Khan NS, Kumar N, Thomas G, Pandey A, Hamurcu M, Gezgin S, Zargar SM, Khan MK. Choudhary S, et al. Curr Top Med Chem. 2024 Mar 27. doi: 10.2174/0115680266274272240321065039. Online ahead of print. Curr Top Med Chem. 2024. PMID: 38551050
Additionally, the study specifically investigated the immunomodulatory properties of Echinacea species extracts using gene expression analysis of GSE12259 from NCBI-GEO through the Bioconductor package GEOquery and limma. RESULTS: A total of 182 studies were comprehensivel …
Additionally, the study specifically investigated the immunomodulatory properties of Echinacea species extracts using gene expression analys …
Identification of Potential Hub Genes Related to Acute Pancreatitis and Chronic Pancreatitis via Integrated Bioinformatics Analysis and In Vitro Analysis.
Yuan L, Liu Y, Fan L, Sun C, Ran S, Huang K, Shen Y. Yuan L, et al. Mol Biotechnol. 2024 Mar 23. doi: 10.1007/s12033-024-01118-5. Online ahead of print. Mol Biotechnol. 2024. PMID: 38520499
Differential gene expression analyses on murine transcriptomes were conducted using the R programming language and the R/Bioconductor package. Additionally, gene network analysis was performed using the STRING database to predict correlations among genes in the context of …
Differential gene expression analyses on murine transcriptomes were conducted using the R programming language and the R/Bioconductor …
PIPETS: A statistically robust, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing.
Furumo Q, Meyer M. Furumo Q, et al. bioRxiv [Preprint]. 2024 Mar 20:2024.03.18.585559. doi: 10.1101/2024.03.18.585559. bioRxiv. 2024. PMID: 38562853 Free PMC article. Preprint.
We present PIPETS, an R package available on Bioconductor that provides a novel analysis approach to study 3'-end sequencing data. ...
We present PIPETS, an R package available on Bioconductor that provides a novel analysis approach to study 3'-end sequencing data. .. …
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications.
Alessandri S, Ratto ML, Rabellino S, Piacenti G, Contaldo SG, Pernice S, Beccuti M, Calogero RA, Alessandri L. Alessandri S, et al. BMC Bioinformatics. 2024 Mar 12;25(1):110. doi: 10.1186/s12859-024-05695-9. BMC Bioinformatics. 2024. PMID: 38475691 Free PMC article.
The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to en …
The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environmen …
1,892 results

Searches related to "bioconductor"