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Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 16 of 16 for “"Bioconductor"”.
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An Empirical Study of API Breaking Changes in Bioconductor
Bioconductor is the second largest R software package repository that is primarily used for the analysis of genomic and biological data. With downloads exceeding millions in recent years, the widespread growth of the repository's adoption can be attributed to it's diverse selection of …
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Análisis de datos de RNA-Seq empleando diferentes paquetes desarrollados dentro del proyecto Bioconductor para estudios de expresión génica diferencial
… la comparación de los tres paquetes del proyecto Bioconductor más populares para el análisis de datos de estudios de expresión génica diferencial: Limma, EdgeR y DESeq2. Para ello, se realizó un exhaustivo análisis de datos procedentes de experimentos reales de RNA-Seq. Las ventajas e …
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Integración de datos ómicos
… R, concretamente a través de paquetes de Bioconductor. Asimismo, la integración de datos se ha efectuado mediante estrategias de análisis multivariante, utilizando este mismo lenguaje de programación. Se ha desarrollado a través de dos aproximaciones diferentes: mínimos cuadrados parciales …
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Investigation of HPV16-related genomic alterations in cervical squamous cell carcinoma
… using R 4.5.1, R Studio, and packages from Bioconductor. Experimental design was created to compare samples with HPV 16 integrated genome with the non-integrated genome. Gene expression involved filtration criteria setting a minimum threshold of 10 counts per gene and 10 samples in each …
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Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework.
… of TFs. Here, I present ChIPanalyser, an R/Bioconductor package that models and predicts binding of TFs to DNA using a statistical thermodynamic framework. First, I show that goodness of fit metrics are an important consideration in TF binding predictions as well as demonstrate …
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Comprehensive analysis of high-throughput experiments for investigating transcription and transcriptional regulation
… details of two such software packages in the Bioconductor project, which I (co-)developed.
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Towards Personalized Medicine Using Systems Biology And Machine Learning
… analysis was released as part of the ROntoTools Bioconductor package.</p>
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Characterization of The Growth Factor Receptor Network Oncogenes in Lung Cancer
… (IGF1R), RAF (RAF1), and KRAS (G12V), using the Bioconductor package, Adaptive Signature Selection and InteGratioN (ASSIGN). Gene lists of various lengths were generated ranging from 5 to 500 genes produced in 25 gene increments. Pathway activation estimates were predicted in 541 lung …
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Estimating transcription factor binding properties in human cell lines using statistical methods and genomics datasets
… of mechanistic processes. ChIPanalyser is an R/Bioconductor package that implements a statistical thermodynamics model for transcription factor binding by leveraging binding motifs, chromatin accessibility and transcription factor concentration. This study aimed to use ChIPanalyser on 135 human …
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Mechanisms of transcription and translation dysfunction in disease: a novel FMRP-translation axis in Alzheimer’s and expansion of Pol III transcription in cancer
… across contexts. The tool interoperates with the Bioconductor ecosystem and is released as a publicly available resource. Chapter 5 synthesizes the main findings, outlines limitations of the experimental and computational approaches, and proposes concrete directions for future work. Together, …
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Unsupervised Signal Deconvolution for Multiscale Characterization of Tissue Heterogeneity
… algorithms, including an R package approved by Bioconductor specifically for tumor-stroma deconvolution. While intercellular heterogeneity is often manifested by multiple clones with distinct sequences, systematic efforts to characterize intercellular genomic heterogeneity must effectively …
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Transcriptional regulation of glycosyltransferase genes in MCF-7 human breast cancer cell line following drug treatment
… initially was counted up to 22,000. Using the Bioconductor open source software in R statistical programming environment a statistical differential expression analysis followed by several data filtering and pre-processing steps were performed to identify up and down regulated GT genes using. …
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BIOLOGICAL AND MOLECULAR CHARACTERIZATION OF CMA-03/06, A NEWLY ESTABLISHED INTERLEUKIN-6 INDEPENDENT VARIANT OF THE CMA-03 HUMAN MYELOMA CELL LINE.
… alterations were calculated using the DNAcopy Bioconductor package, based on circular binary segmentation method. Global gene expression profiling (GEP) was performed by means of the GeneChip Human Gene 1.0 ST Arrays (Affymetrix); the supervised analyses were done using the rank Prod method and …
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Systems Biology of Host-Pathogen Protein-Protein Interactions
… alternative, in Chapter 4, we developed a R/Bioconductor package, HPiP software with a series of amino acid sequence property descriptors and an ensemble machine learning classifiers to predict the yet unmapped interactions between pathogen and host proteins. Using SARS-CoV-1 or the novel …
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Biogenesis and Function of the Mitochondrial Ribosome
… implemented in R and is freely available as the Bioconductor package ComPrAn. It provides tools for analysis of peptide-level data as well as normalisation and clustering tools for protein-level data, dedicated visualisation functions and is accompanied by a graphical user interface. Throughout …
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A Comparison of Microarray Analyses: A Mixed Models Approach Versus the Significance Analysis of Microarrays
DNA microarrays are a relatively new technology for assessing the expression levels of thousands of genes simultaneously. Researchers hope to find genes that are differentially expressed by hybridizing cDNA from known treatment sources with various genes spotted on the microarrays. The large number …