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   Articles with "bioconductor" as a keyword



Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data

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recommendations! Published in 2021 at "Computational and Structural Biotechnology Journal"

DOI: 10.1016/j.csbj.2021.05.022

Abstract: Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover,… read more here.

Keywords: genome scale; cytoscape; bioconductor; mechanistic modeling ... See more keywords

Orchestrating chromosome conformation capture analysis with Bioconductor

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recommendations! Published in 2024 at "Nature Communications"

DOI: 10.1038/s41467-024-44761-x

Abstract: Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational… read more here.

Keywords: bioconductor; chromosome conformation; conformation capture; conformation ... See more keywords

Invited Commentary: Improving the Accessibility of Human Microbiome Project Data Through Integration With R/Bioconductor.

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recommendations! Published in 2019 at "American journal of epidemiology"

DOI: 10.1093/aje/kwz007

Abstract: Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference data set of the "normal" human microbiome of 242 healthy adults at 5… read more here.

Keywords: human microbiome; bioconductor; microbiome project; microbiome ... See more keywords

StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac042

Abstract: Abstract Summary StructuralVariantAnnotation is an R/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the… read more here.

Keywords: caller agnostic; ecosystem; bioconductor; structural variant ... See more keywords

scanMiR: a biochemically-based toolkit for versatile and efficient microRNA target prediction.

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recommendations! Published in 2022 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btac110

Abstract: MOTIVATION microRNAs are important post-transcriptional regulators of gene expression, but the identification of functionally relevant targets is still challenging. Recent research has shown improved prediction of microRNA-mediated repression using a biochemical model combined with empirically-derived… read more here.

Keywords: microrna; bioconductor; scanmir; prediction ... See more keywords

BRGenomics for analyzing high resolution genomics data in R.

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recommendations! Published in 2023 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btad331

Abstract: 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. Utilizing GenomicRanges and other core Bioconductor… read more here.

Keywords: brgenomics analyzing; resolution genomics; bioconductor; genomics data ... See more keywords

Mariner: explore the Hi-Cs

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recommendations! Published in 2024 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btae352

Abstract: Abstract Motivation 3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable… read more here.

Keywords: mariner; mariner explore; bioconductor;

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC

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recommendations! Published in 2018 at "Bioinformatics"

DOI: 10.1093/bioinformatics/bty124

Abstract: Motivation: The large‐scale multidimensional omics data in the Genomic Data Commons (GDC) provides opportunities to investigate the crosstalk among different RNA species and their regulatory mechanisms in cancers. Easy‐to‐use bioinformatics pipelines are needed to facilitate… read more here.

Keywords: package; gdcrnatools bioconductor; data gdc; bioconductor ... See more keywords

ggCyto: next generation open-source visualization software for cytometry

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recommendations! Published in 2018 at "Bioinformatics"

DOI: 10.1093/bioinformatics/bty441

Abstract: Motivation Open source software for computational cytometry has gained in popularity over the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have highlighted the importance of efforts to standardize both experimental… read more here.

Keywords: open source; bioconductor; cytometry data; cytometry ... See more keywords

RTNsurvival: an R/Bioconductor package for regulatory network survival analysis

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recommendations! Published in 2019 at "Bioinformatics"

DOI: 10.1093/bioinformatics/btz229

Abstract: MOTIVATION Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets.… read more here.

Keywords: package; network; rtnsurvival bioconductor; regulon ... See more keywords

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

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recommendations! Published in 2019 at "BMC Bioinformatics"

DOI: 10.1186/s12859-019-2879-1

Abstract: BackgroundPrincipal component analysis (PCA) is frequently used in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed… read more here.

Keywords: package; pcaexplorer bioconductor; bioconductor; rna seq ... See more keywords