Metagenomics Bioinformatics
Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis.
Scientific topics: Metagenomics
Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology
Resource type: Tutorial
Metagenomics Bioinformatics
https://www.ebi.ac.uk/training/online/course/metagenomics-bioinformatics
http://tess.elixir-uk.org/materials/metagenomics-bioinformatics
Metagenomics, the genomic analysis of microbial communities from samples like water and soil, involves high throughput sequencing of the microbial DNA, collecting, archiving and resharing the genomic data for taxonomic and functional analysis.
Alex Mitchell
Varsha Kale
Rob Finn
Guillermo Rangel Pineros
Rebecca Campos
Alex Mitchell
Varsha Kale
Rob Finn
Guillermo Rangel Pineros
Rebecca Campos
Metagenomics
Metagenomics, MGnify, Sequence Analysis, Microbiology
Life Scientists
EBI Metagenomics: analysing and exploring metagenomics data
EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets...
Scientific topics: Metagenomics
Keywords: Metagenomics, MGnify, Sequence Analysis, Microbiology
Resource type: Webinar
EBI Metagenomics: analysing and exploring metagenomics data
https://www.ebi.ac.uk/training/online/course/ebi-metagenomics-analysing-and-exploring-metagenomics-data
http://tess.elixir-uk.org/materials/ebi-metagenomics-analysing-and-exploring-metagenomics-data
EBI metagenomics is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly datasets. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive.
Alex Mitchell
Alex Mitchell
Metagenomics
Metagenomics, MGnify, Sequence Analysis, Microbiology
Life Scientists
Analysing and visualising microbiome-derived datasets using the MGnify Web API
MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available...
Analysing and visualising microbiome-derived datasets using the MGnify Web API
https://www.ebi.ac.uk/training/online/course/analysing-and-visualising-microbiome-derived-datasets-using-mgnify-web-api
http://tess.elixir-uk.org/materials/analysing-and-visualising-microbiome-derived-datasets-using-the-mgnify-web-api
MGnify (formerly EBI Metagenomics) is a freely available hub for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. The resource provides rich functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets drawn from the European Nucleotide Archive (ENA).
Liftr & sbgr
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, 1560 software packages, and an...
Liftr & sbgr
https://bioconductor.org/BioC2015/#ami
http://tess.elixir-uk.org/materials/detecting-differential-binding-in-chip-seq-data-with-csaw-7a3a67bf-a44b-4bcb-a54f-02412e71104c
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Nan Xiao
Workflows
Discussion: Guidelines for submitting data to ExperimentHub
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, 1560 software packages, and an...
Discussion: Guidelines for submitting data to ExperimentHub
https://bioconductor.org/help/course-materials/2019/BiocDevelForum/03-ExperimentHub.pdf
http://tess.elixir-uk.org/materials/discussion-guidelines-for-submitting-data-to-experimenthub
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Stephanie Hicks
HCA Data Access
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, 1560 software packages, and an...
HCA Data Access
https://bioconductor.org/help/course-materials/2019/HCA/HCA_Data_Access.pptx
http://tess.elixir-uk.org/materials/hca-data-access
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Daniel van Twisk
Single cell updates
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, 1560 software packages, and an...
Single cell updates
https://bioconductor.org/help/course-materials/2019/BiocDevelForum/01-SingleCell.pptx
http://tess.elixir-uk.org/materials/single-cell-updates
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Aaron Lun
Pitfalls and best practices for serializing Bioconductor objects
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, 1560 software packages, and an...
Pitfalls and best practices for serializing Bioconductor objects
https://bioconductor.org/help/course-materials/2019/BiocDevelForum/02-Serialization.pdf
http://tess.elixir-uk.org/materials/pitfalls-and-best-practices-for-serializing-bioconductor-objects
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Lori Shepherd
Introduction to DataFrames and the impact of recent changes
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, 1560 software packages, and an...
Introduction to DataFrames and the impact of recent changes
https://bioconductor.org/help/course-materials/2019/BiocDevelForum/02-DataFrame.pdf
http://tess.elixir-uk.org/materials/introduction-to-dataframes-and-the-impact-of-recent-changes
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Hervé Pagès
Evening session: Efficient R
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, 1560 software packages, and an...
Evening session: Efficient R
https://bioconductor.org/help/course-materials/2019/CSAMA/efficient_r.html
http://tess.elixir-uk.org/materials/evening-session-efficient-r
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Big data
Lab 9-1: Efficient and Parallel Evaluation
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, 1560 software packages, and an...
Lab 9-1: Efficient and Parallel Evaluation
https://bioconductor.org/help/course-materials/2019/CSAMA/L9.1-efficient-and-parallel-r.html
http://tess.elixir-uk.org/materials/lab-9-1-efficient-and-parallel-evaluation
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Big data
Lecture 20-1: Working with Large Data
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, 1560 software packages, and an...
Lecture 20-1: Working with Large Data
https://bioconductor.org/help/course-materials/2019/CSAMA/lecture-20-1-big-data.html
http://tess.elixir-uk.org/materials/lecture-20-1-working-with-large-data
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Big data
Lecture 19: Gene Set Enrichment Analysis
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, 1560 software packages, and an...
Lecture 19: Gene Set Enrichment Analysis
https://bioconductor.org/help/course-materials/2019/CSAMA/lecture-19-gene-set-enrichment.pdf
http://tess.elixir-uk.org/materials/lecture-19-gene-set-enrichment-analysis
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
GSEA
Lab 1: Introduction to R and Bioconductor
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, 1560 software packages, and an...
Lab 1: Introduction to R and Bioconductor
https://bioconductor.org/help/course-materials/2019/CSAMA/lab-1-intro-to-r-bioc.html
http://tess.elixir-uk.org/materials/lab-1-introduction-to-r-and-bioconductor
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
introduction
Lecture 1: Introduction to R and Bioconductor
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, 1560 software packages, and an...
Lecture 1: Introduction to R and Bioconductor
https://bioconductor.org/help/course-materials/2019/CSAMA/lecture-01-r-intro.html
http://tess.elixir-uk.org/materials/lecture-1-introduction-to-r-and-bioconductor
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
introduction
06: Gene Set Enrichment Analysis
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, 1560 software packages, and an...
06: Gene Set Enrichment Analysis
https://bioconductor.org/help/course-materials/2019/BSS2019/06_GeneSetEnrichment.html
http://tess.elixir-uk.org/materials/06-gene-set-enrichment-analysis
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
06: Gene Set Enrichment -- Introduction
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, 1560 software packages, and an...
06: Gene Set Enrichment -- Introduction
https://bioconductor.org/help/course-materials/2019/BSS2019/06_GeneSetEnrichmentSlides.pdf
http://tess.elixir-uk.org/materials/06-gene-set-enrichment-introduction
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
05: Bioconductor Annotation Resources
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, 1560 software packages, and an...
05: Bioconductor Annotation Resources
https://bioconductor.org/help/course-materials/2019/BSS2019/05_Annotations.html
http://tess.elixir-uk.org/materials/05-bioconductor-annotation-resources
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
04: Practical: Organizing data with SummarizedExperiment
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, 1560 software packages, and an...
04: Practical: Organizing data with SummarizedExperiment
https://bioconductor.org/help/course-materials/2019/BSS2019/04_Practical_CoreApproachesInBioconductor.html
http://tess.elixir-uk.org/materials/04-practical-organizing-data-with-summarizedexperiment
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
03: Core approaches in Bioconductor
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, 1560 software packages, and an...
03: Core approaches in Bioconductor
https://bioconductor.org/help/course-materials/2019/BSS2019/03_CoreApproachesInBioconductor.html
http://tess.elixir-uk.org/materials/03-core-approaches-in-bioconductor
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
02: Practical: R / Bioconductor and Reproducible Research
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, 1560 software packages, and an...
02: Practical: R / Bioconductor and Reproducible Research
https://bioconductor.org/help/course-materials/2019/BSS2019/02_Practical_RBioconductorAndReproductibleResearch.html
http://tess.elixir-uk.org/materials/02-practical-r-bioconductor-and-reproducible-research
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
01: Introduction to R and Bioconductor
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, 1560 software packages, and an...
01: Introduction to R and Bioconductor
https://bioconductor.org/help/course-materials/2019/BSS2019/01_IntroToRAndBioconductor.html
http://tess.elixir-uk.org/materials/01-introduction-to-r-and-bioconductor
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Intro
Developing robust and efficient code
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, 1560 software packages, and an...
Developing robust and efficient code
https://bioconductor.org/help/course-materials/2019/NURDS/NURDS.html
http://tess.elixir-uk.org/materials/developing-robust-and-efficient-code
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Martin Morgan
Workshop
Working with DNA Sequences
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, 1560 software packages, and an...
Keywords: Data Representation
Working with DNA Sequences
https://bioconductor.org/help/course-materials/2014/SeattleFeb2014/Bioconductor_sequences.pdf
http://tess.elixir-uk.org/materials/genomic-ranges-slides
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Sonali Arora
Data Representation
RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression
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, 1560 software packages, and an...
Scientific topics: RNA-Seq
RNA-Seq Lab: Workflow -- gene-level exploratory analysis and differential expression
https://bioconductor.org/help/workflows/rnaseqGene/
http://tess.elixir-uk.org/materials/rna-seq-lab-workflow-gene-level-exploratory-analysis-and-differential-expression
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Michael Love et al.
RNA-Seq
Multiple testing
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, 1560 software packages, and an...
Scientific topics: Statistics and probability
Multiple testing
https://bioconductor.org/help/course-materials/2016/CSAMA/lect-02+13-testing/160711-brixen-testing-huber.pdf
http://tess.elixir-uk.org/materials/hypothesis-testing-27ffb208-e582-48db-a8c0-ad22a87a1329
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, 1560 software packages, and an active user community.
Bioconductor is also available as an AMI (Amazon Machine Image) and a series of Docker images.
Wolfgang Huber
Statistics and probability
