21 materials found

Keywords:

RNA-seq module Frederik Coppens

Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128 Material concerning RNA-seq analysis, with an emphasis on the statistical aspects. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Analysis of variance

You already know a good bit about hypothesis testing with one or two samples. Now we take things further by making inferences based on three or more samples. We'll use the very special F-distribution to do it (F stands for "fabulous").

Keywords: Inferential statistics

Analysis of variance https://tess.elixir-europe.org/materials/analysis-of-variance You already know a good bit about hypothesis testing with one or two samples. Now we take things further by making inferences based on three or more samples. We'll use the very special F-distribution to do it (F stands for "fabulous"). Inferential statistics 2016-08-14
Chi-square probability distribution

You've gotten good at hypothesis testing when you can make assumptions about the underlying distributions. In this tutorial, we'll learn about a new distribution (the chi-square one) and how it can help you (yes, you) infer what an underlying distribution even is!

Keywords: Inferential statistics

Chi-square probability distribution https://tess.elixir-europe.org/materials/chi-square-probability-distribution You've gotten good at hypothesis testing when you can make assumptions about the underlying distributions. In this tutorial, we'll learn about a new distribution (the chi-square one) and how it can help you (yes, you) infer what an underlying distribution even is! Inferential statistics 2016-08-14
Hypothesis testing with two samples

You're already familiar with hypothesis testing with one sample. In this tutorial, we'll go further by testing whether the difference between the means of two samples seems to be unlikely purely due to chance.

Keywords: Inferential statistics

Hypothesis testing with two samples https://tess.elixir-europe.org/materials/hypothesis-testing-with-two-samples You're already familiar with hypothesis testing with one sample. In this tutorial, we'll go further by testing whether the difference between the means of two samples seems to be unlikely purely due to chance. Inferential statistics 2016-08-14
Hypothesis testing with one sample

This tutorial helps us answer one of the most important questions not only in statistics, but all of science: how confident are we that a result from a new drug or process is not due to random chance but due to an actual impact. If you are familiar with sampling distributions and confidence...

Keywords: Inferential statistics

Hypothesis testing with one sample https://tess.elixir-europe.org/materials/hypothesis-testing-with-one-sample This tutorial helps us answer one of the most important questions not only in statistics, but all of science: how confident are we that a result from a new drug or process is not due to random chance but due to an actual impact. If you are familiar with sampling distributions and confidence intervals, you're ready for this adventure! Inferential statistics 2016-08-14
Bernoulli distributions and margin of error

Ever wondered what pollsters are talking about when they said that there is a 3% "margin of error" in their results. Well, this tutorial will not only explain what it means, but give you the tools and understanding to be a pollster yourself!

Keywords: Inferential statistics

Bernoulli distributions and margin of error https://tess.elixir-europe.org/materials/bernoulli-distributions-and-margin-of-error Ever wondered what pollsters are talking about when they said that there is a 3% "margin of error" in their results. Well, this tutorial will not only explain what it means, but give you the tools and understanding to be a pollster yourself! Inferential statistics 2016-08-14
Confidence intervals

We all have confidence intervals ("I'm the king of the world!!!!") and non-confidence intervals ("No one loves me"). That is not what this tutorial is about. This tutorial takes what you already know about the central limit theorem, sampling distributions, and z-scores and uses these tools to...

Keywords: Inferential statistics

Confidence intervals https://tess.elixir-europe.org/materials/confidence-intervals We all have confidence intervals ("I'm the king of the world!!!!") and non-confidence intervals ("No one loves me"). That is not what this tutorial is about. This tutorial takes what you already know about the central limit theorem, sampling distributions, and z-scores and uses these tools to dive into the world of inferential statistics. It may seem magical at first, but from our sample, we can now make inferences about the probability of our population mean actually being in an interval. Inferential statistics 2016-08-14
Sampling distribution

In this tutorial, we experience one of the most exciting ideas in statistics--the central limit theorem. Without it, it would be a lot harder to make any inferences about population parameters given sample statistics. It tells us that, regardless of what the population distribution looks like,...

Keywords: Inferential statistics

Sampling distribution https://tess.elixir-europe.org/materials/sampling-distribution In this tutorial, we experience one of the most exciting ideas in statistics--the central limit theorem. Without it, it would be a lot harder to make any inferences about population parameters given sample statistics. It tells us that, regardless of what the population distribution looks like, the distribution of the sample means (you'll learn what that is) can be normal. Good idea to understand a bit about normal distributions before diving into this tutorial. Inferential statistics 2016-08-14
Normal distribution

The normal distribution (often referred to as the "bell curve" is at the core of most of inferential statistics. By assuming that most complex processes result in a normal distribution (we'll see why this is reasonable), we can gauge the probability of it happening by chance. To best enjoy this...

Keywords: Inferential statistics

Normal distribution https://tess.elixir-europe.org/materials/normal-distribution The normal distribution (often referred to as the "bell curve" is at the core of most of inferential statistics. By assuming that most complex processes result in a normal distribution (we'll see why this is reasonable), we can gauge the probability of it happening by chance. To best enjoy this tutorial, it is good to come to it understanding what probability distributions and random variables are. You should also be very familiar with the notions of population and sample mean and standard deviation. Inferential statistics 2016-08-14
Variant-calling

No description available

Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
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
Statistics and RNA-Seq

This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

Statistics and RNA-Seq https://tess.elixir-europe.org/materials/statistics-and-rna-seq This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Material for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis.

Scientific topics: RNA-Seq

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

Material for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/material-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. RNA-Seq RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
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
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
Material provided by Charlotte Soneson

This folder contains material provided by Charlotte Soneson. The following material is included:

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Eija Korpelainen

All material concerning RNA-seq data analysis with Chipster

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

RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

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

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
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
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

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

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exploratory analysis and downstream analysis

This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

Keywords: Statistical-model, Exploratory-analysis

Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis