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23 materials found

Authors: Christine Staiger  or Bernardo Clavijo  or Jenny Drnevich @jenny 


Introduction to Persistent Identifiers

Module also available as self-study material in data carpentry style

Scientific topics: Data management

Keywords: system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers

Resource type: course materials

Introduction to Persistent Identifiers https://tess.elixir-europe.org/materials/introduction-to-persistent-identifiers Module also available as self-study material in data carpentry style Data management system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers data stewards data managers bioinformaticians
Helis Academy - Persistent identifiers and their use cases

Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source

Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management

Resource type: Slides

Helis Academy - Persistent identifiers and their use cases https://tess.elixir-europe.org/materials/persistent-identifiers-and-their-use-cases Managing increasing numbers of data objects Sharing data from different sourcesamongst researchers Data needs to be (globally) identifiable and addressable to ensure reuse of data Data citation Linking data from different source Referencing data and code, Findability of data and code, Identifying data and code, data management data stewards Life Science Researchers bioinformaticians
Helis Academy - Data Sharing, publishing and archiving

Basic knowledge of: o Know what a repository is o Characteristics of Data Sharing, Archiving and Publishing o Knowledge of major platforms for Sharing, Archiving and Publishing Hands on experience: o Dataverse possibilities for sharing and publishing o Designing requirements digital...

Keywords: data sharing, Data publishing, data archiving, data repositories, data management

Resource type: Slides

Helis Academy - Data Sharing, publishing and archiving https://tess.elixir-europe.org/materials/data-sharing-publishing-and-archiving Basic knowledge of: o Know what a repository is o Characteristics of Data Sharing, Archiving and Publishing o Knowledge of major platforms for Sharing, Archiving and Publishing Hands on experience: o Dataverse possibilities for sharing and publishing o Designing requirements digital archives o Finding your ideal archive data sharing, Data publishing, data archiving, data repositories, data management
Introduction to FAIR data stewardship

FAIR data Stewardship: How to improve the reuse of nanosafety data

Scientific topics: Data management

Keywords: FAIR

Introduction to FAIR data stewardship https://tess.elixir-europe.org/materials/introduction-to-fair-data-stewardship FAIR data Stewardship: How to improve the reuse of nanosafety data Data management FAIR Life Science Researchers
FAIR Data Stewardship - Data sharing, archiving and publishing

The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities...

Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

Resource type: Slides, Training materials

FAIR Data Stewardship - Data sharing, archiving and publishing https://tess.elixir-europe.org/materials/fair-data-stewardship-data-sharing-archiving-and-publishing The workshop introduces the concepts and gives hands-on experience with tools which allow safe data sharing, archiving and publishing on example services. Moreover, participants of the workshop explore together different roles which are defined around data publication and how responsibilities towards data are distributed. The course does not require any prior knowledge. Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication General Interest Scientists Researchers data stewards
Introduction to R and Bioconductor lecture

This reference handout goes over how to read and parse a line of complex R code.

Keywords: R-programming

Introduction to R and Bioconductor lecture https://tess.elixir-europe.org/materials/introduction-to-r-and-bioconductor-lecture-990e00de-2241-49f5-9577-5c110cc06a64 This reference handout goes over how to read and parse a line of complex R code. R-programming
Genome assembly and validation

Course materials from the 2015 de novo course.

Keywords: Earlham Institute

Genome assembly and validation https://tess.elixir-europe.org/materials/genome-assembly-and-validation Course materials from the 2015 de novo course. Earlham Institute
Data QC and preparation

Course materials from the data QC and preparation course.

Keywords: Earlham Institute

Data QC and preparation https://tess.elixir-europe.org/materials/data-qc-and-preparation Course materials from the data QC and preparation course. Earlham Institute
A simple genome assembly

Course materials from the 2015 De Novo course.

Keywords: Earlham Institute

A simple genome assembly https://tess.elixir-europe.org/materials/a-simple-genome-assembly Course materials from the 2015 De Novo course. Earlham Institute
First pass assembly and QC

Course materials from the 2015 De Novo course.

Keywords: Earlham Institute

First pass assembly and QC https://tess.elixir-europe.org/materials/first-pass-assembly-and-qc Course materials from the 2015 De Novo course. Earlham Institute
Sequencing Technologies

Course materials from the 2015 de novo course.

Scientific topics: Sequencing

Keywords: De Novo, Earlham Institute

Sequencing Technologies https://tess.elixir-europe.org/materials/sequencing-technologies Course materials from the 2015 de novo course. Sequencing De Novo, Earlham Institute
SeqAhead: NGS current challenges and data analysis for plant researchers

Complete course materials from the 2014 NGS course.

Keywords: next generation sequencing, Earlham Institute

SeqAhead: NGS current challenges and data analysis for plant researchers https://tess.elixir-europe.org/materials/seqahead-ngs-current-challenges-and-data-analysis-for-plant-researchers Complete course materials from the 2014 NGS course. next generation sequencing, Earlham Institute
Guide to R swirl interactive lessons

This handout describes how to download the swirl package and start the basic interactive lessons to learn R.

Keywords: R-programming

Guide to R swirl interactive lessons https://tess.elixir-europe.org/materials/guide-to-r-swirl-interactive-lessons This handout describes how to download the swirl package and start the basic interactive lessons to learn R. R-programming
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Introduction to R practice codes

These codes give an overview of R object types and programming language structure.

Keywords: R-programming

Introduction to R practice codes https://tess.elixir-europe.org/materials/introduction-to-r-practice-codes These codes give an overview of R object types and programming language structure. R-programming
R/Bioconductor installation and upgrade guide

This handout describes how to download R and install add-on packages, both from CRAN and

Keywords: R-programming

R/Bioconductor installation and upgrade guide https://tess.elixir-europe.org/materials/r-bioconductor-installation-and-upgrade-guide This handout describes how to download R and install add-on packages, both from CRAN and R-programming
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
Intro to R and Bioconductor

R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the...

Keywords: Prerequisite, R-programming

Intro to R and Bioconductor https://tess.elixir-europe.org/materials/intro-to-r-and-bioconductor R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data. This module covers the basic skills that will be needed before using R to analyze NGS data. Prerequisite, R-programming
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
Introduction to R and Bioconductor lecture

This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure.

Keywords: R-programming

Introduction to R and Bioconductor lecture https://tess.elixir-europe.org/materials/introduction-to-r-and-bioconductor-lecture This lecture gives an overview of the R and Bioconductor projects, plus the basics of R object types and programming language structure. R-programming
Day 1 - RNA-Seq Analysis

Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer.

Keywords: Alignment, BAM, FASTA, FASTQ, QC

Day 1 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-1-rna-seq-analysis Day 1 starts at the very beginning of a typical RNA-Seq workflow, explaining the sequencing technology and considerations for experimental design, then starts with hands-on application of working with sequencing data fresh off the sequencer. Alignment, BAM, FASTA, FASTQ, QC
Data objects for R practice codes

This RData file contains small R objects to use in the [introR.R practice questions](introR.R)

Keywords: R-programming

Data objects for R practice codes https://tess.elixir-europe.org/materials/data-objects-for-r-practice-codes This RData file contains small R objects to use in the [introR.R practice questions](introR.R) R-programming
Day 2 - RNA-Seq Analysis

Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing