- Видео 334
- Просмотров 251 415
Bioconductor
Добавлен 24 июл 2014
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 800+ software packages, and an active user community. Bioconductor is also available as an Amazon Machine Image (AMI).
This channel contains short, single-topic videos as an interactive complement to traditional vignettes and workflows .
The plan is to create a series of 5 minute videos that encapsulate a HOWTO skill or overview a project aspect.
This channel contains short, single-topic videos as an interactive complement to traditional vignettes and workflows .
The plan is to create a series of 5 minute videos that encapsulate a HOWTO skill or overview a project aspect.
Workshop: High-Performance Computing in R for Genomic Research
High-Performance Computing in R for Genomic Research**
Author(s): Jiefei Wang
Affiliation(s): University at Texas Medical Branch
High-performance computing(HPC) has become an essential topic for handling large high-throughput data and bringing complex algorithms to life. However, the intricate nature of parallelization structures often hinders people from implementing the correct parallel computing cluster in R. In this talk, we will introduce the modern parallel framework package BiocParallel and its utility packages SharedObject and RedisParam. During our exploration of High-performance computing in R, we will dive into a variety of important topics, covering both foundational principles a...
Author(s): Jiefei Wang
Affiliation(s): University at Texas Medical Branch
High-performance computing(HPC) has become an essential topic for handling large high-throughput data and bringing complex algorithms to life. However, the intricate nature of parallelization structures often hinders people from implementing the correct parallel computing cluster in R. In this talk, we will introduce the modern parallel framework package BiocParallel and its utility packages SharedObject and RedisParam. During our exploration of High-performance computing in R, we will dive into a variety of important topics, covering both foundational principles a...
Просмотров: 545
Видео
Short Talks: Single cell
Просмотров 34511 месяцев назад
ruclips.net/video/zcUMq9ZAOnw/видео.htmlfeature=shared&t=82 Unraveling Immunogenomic Diversity in Single-Cell Data ruclips.net/video/zcUMq9ZAOnw/видео.htmlfeature=shared&t=864 Model-based Dimensionality Reduction for Single-cell RNA-seq with Generalized Bilinear Models ruclips.net/video/zcUMq9ZAOnw/видео.htmlfeature=shared&t=1723 Interactive analysis of single-cell data using flexible workflows...
Workshop: Voyager: Exploratory spatial data analysis from geospatial to spatial -omics
Просмотров 27111 месяцев назад
Voyager: Exploratory spatial data analysis from geospatial to spatial -omics Author(s): Lambda Moses,Kayla Jackson,Laura Luebbert,Pétur Helgi Einarsson,Pall Melsted,Lior Pachter Affiliation(s): California Institute of Technology Social media: LambdaMoses With the rise of spatial transcriptomics, many methods have been written for specialized tasks in spatial transcriptomics data ana...
Package demo: demuxSNP: supervised demultiplexing of scRNAseq data using cell hashing and SNPs
Просмотров 22611 месяцев назад
demuxSNP: supervised demultiplexing of scRNAseq data using cell hashing and SNPs Author(s): Michael P Lynch,Laurent Gatto,Aedin C Culhane Affiliation(s): University of Limerick Social media: AedinCulhane Sequencing at a single-cell resolution allows unprecedented understanding of biologically relevant differences between individual cells compared to previous bulk methods. Though the...
Keynote: Nancy Zhang, Tumor subclone detection and immune niche modeling on spatial transcriptomics
Просмотров 30811 месяцев назад
Nancy Zhang Professor of Statistics and Data Science, University of Pennsylvania Dr. Zhang is Professor of Statistics and Data Science in The Wharton School at University of Pennsylvania. Her current research focuses primarily on the development of statistical and computational approaches for the analysis of genetic, genomic, and transcriptomic data. In the field of Genomics, she has developed ...
Package demo: Differential Expression Analysis using Limma and qsvaR
Просмотров 82511 месяцев назад
Differential Expression Analysis using Limma and qsvaR Author(s): Hedia Tnani,Joshua M. Stolz,Leonardo Collado-Torres,Louise A. Huuki-Myers,Leonardo Collado Torres Affiliation(s): Lieber Institute for Brain Development Social media: TnaniHedia RNA-seq and its expression levels are vulnerable to both environmental and technical influences. In previous studies that explored gene expre...
Keynote: Heng Li, Genome assembly in the telomere-to-telomere era
Просмотров 47711 месяцев назад
Heng Li Associate Professor, Dana-Farber Cancer Institute and Harvard Medical School Heng Li studies advanced computational algorithms to solve practical biological problems, currently with a focus on sequence alignment, variant calling, de novo assembly, data storage, and information query. He developed and maintains several widely used software packages, such as BWA, samtools, minimap2, and s...
Meet the BioC teams, TAB,
Просмотров 4111 месяцев назад
ruclips.net/video/_peGjCcfvLQ/видео.htmlfeature=shared&t=90 Meet the Technical Advisory Board (TAB) The Technical Advisory Board purpose is to support the Bioconductor mission by developing strategies to ensure long-term technical suitability of core infrastructure for the Bioconductor mission. Core infrastructure includes: all aspects of package addition, management, and distribution; end-user...
Package demo: Tidy genomic and transcriptomic single cell analyses
Просмотров 12611 месяцев назад
Tidy genomic and transcriptomic single-cell analyses Author(s): Stefano Mangiola,Michael I Love Affiliation(s): WEHI Social media: steman_research This workshop will present how to perform genomic and transcriptomic data analysis using the tidy data paradigm. This paradigm became the standard in R data analysis across many fields. It provides a standard way to organise data values, ...
Package demo: Isoformic: Isoform level biological interpretation from transcriptomic data
Просмотров 8511 месяцев назад
Isoformic: Isoform level biological interpretation from transcriptomic data Author(s): Izabela Mamede Conceição,Lucio Rezende Queiroz,Thomaz Luscher Dias,Julia Raspante Martins,Nayara Evelin de Toledo,Gloria Regina Franco Affiliation(s): Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil Social media: twitter.c...
Package demo: Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Просмотров 8311 месяцев назад
Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2 Author(s): Yingxin Lin,Yue Cao,Elijah Willie,Ellis Patrick,Jean Yang Affiliation(s): The University of Sydney The recent emergence of multi-sample multi-condition single-cell multi-cohort studies allows researchers to investigate different cell states. The effective integration of multiple large-cohort studies ...
Short Talks Microbiome, Proteomics Fri edited
Просмотров 5311 месяцев назад
ruclips.net/video/JM_w32oXe3s/видео.htmlfeature=shared&t=116 Orchestrating microbiome multi-omics with R/Bioconductor ruclips.net/video/JM_w32oXe3s/видео.htmlfeature=shared&t=747 Linear models and empirical Bayes methods for proteome-wide label-free quantification and differential expression in mass spectrometry-based proteomics experiments ruclips.net/video/JM_w32oXe3s/видео.htmlfeature=shared...
Workshop: Mariner: Explore the Hi-Cs
Просмотров 8811 месяцев назад
Mariner: Explore the Hi-Cs Author(s): Eric Scott Davis,Manjari Kiran,Sarah M Parker,Nicole Kramer,Douglas Phanstiel Affiliation(s): The University of North Carolina at Chapel Hill Social media: ericscottdavis1 3D chromatin structure plays an integral, yet incompletely understood role in the long-distance regulation of genes by enhancers and repressors. Disruption or aberrant formati...
Package demo: A shiny application for single cell RNA-seq visualization
Просмотров 42911 месяцев назад
A shiny application for single cell RNA-seq visualization Author(s): Jianhong Ou Affiliation(s): Duke Regeneration Center, Duke University Social media: gaziou Single-cell RNA sequencing (scRNA-seq) is a powerful technique to study gene expression, cellular heterogeneity, and cell states within samples in single-cell level. The development of scRNA-seq shed light to address the know...
Short talks: Infrastructure
Просмотров 3711 месяцев назад
ruclips.net/video/-8vBQ6KYU1A/видео.htmlfeature=shared&t=0 GHA-Built: Building binaries for R/Bioconductor packages via Github Actions ruclips.net/video/-8vBQ6KYU1A/видео.htmlfeature=shared&t=966 MultimodalExperiment: Integrative Bulk and Single-Cell Experiment Container ruclips.net/video/-8vBQ6KYU1A/видео.htmlfeature=shared&t=1677 AnVILWorkflow: A runnable workflow package for Cloud-implemente...
Package demo: Multi-omic Integration and Analysis of cBioPortal and TCGA data MultiAssayExperiment
Просмотров 20711 месяцев назад
Package demo: Multi-omic Integration and Analysis of cBioPortal and TCGA data MultiAssayExperiment
Short Talks: Spatial Transcriptomics
Просмотров 17511 месяцев назад
Short Talks: Spatial Transcriptomics
Keynote: Jeff Moffitt, Genome-scale imaging of the microbiome-host interface with MERFISH
Просмотров 21811 месяцев назад
Keynote: Jeff Moffitt, Genome-scale imaging of the microbiome-host interface with MERFISH
BOF: Bioconductor Carpentries global teaching
Просмотров 3511 месяцев назад
BOF: Bioconductor Carpentries global teaching
Package demo: Orchestrating Hi C analysis with Bioconductor
Просмотров 23711 месяцев назад
Package demo: Orchestrating Hi C analysis with Bioconductor
Workshop: Reproducible and programmatic analysis of flow cytometry experiments with the cytoverse
Просмотров 23711 месяцев назад
Workshop: Reproducible and programmatic analysis of flow cytometry experiments with the cytoverse
Package demo: rGREAT: an R/Bioconductor Package for Functional Enrichment on Genomic Regions
Просмотров 24211 месяцев назад
Package demo: rGREAT: an R/Bioconductor Package for Functional Enrichment on Genomic Regions
Package demo: Epidemiology for Bioinformaticians
Просмотров 4811 месяцев назад
Package demo: Epidemiology for Bioinformaticians
Keynote: Beth Cimini, Making more from your microscopy
Просмотров 15811 месяцев назад
Keynote: Beth Cimini, Making more from your microscopy
Workshop: Bridges from python to Bioconductor: applications in genetics and single-cell genomics
Просмотров 6711 месяцев назад
Workshop: Bridges from python to Bioconductor: applications in genetics and single-cell genomics
Workshop: A Bioconductor-style differential expression analysis powered by SPEAQeasy
Просмотров 13811 месяцев назад
Workshop: A Bioconductor-style differential expression analysis powered by SPEAQeasy
Thanks for your job