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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Benilton_Carvalho/README.md
http://tess.elixir-uk.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128
Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.
Benilton Carvalho @benilton
FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/Variant-calling/README.md
http://tess.elixir-uk.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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Jenny_Drnevich/Day4.md
http://tess.elixir-uk.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.
Jenny Drnevich @jenny
Radhika Khetani @radhika
Jessica Kirkpatrick krkptrc2@illinois.edu
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Benilton_Carvalho/StatsRNASeq.md
http://tess.elixir-uk.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.
Benilton Carvalho @benilton
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Eija_Korpelainen/RNAseq_data_analysis_with_Chipster_2015.md
http://tess.elixir-uk.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.
Eija Korpelainen @eija, ekorpelainen@gmail.com
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Jenny_Drnevich/Day3.md
http://tess.elixir-uk.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.
Jenny Drnevich @jenny
Radhika Khetani @radhika
Jessica Kirkpatrick krkptrc2@illinois.edu
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Jenny_Drnevich/README.md
http://tess.elixir-uk.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
Jenny Drnevich @jenny
Radhika Khetani @radhika
Jessica Kirkpatrick krkptrc2@illinois.edu
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Charlotte_Soneson/README.md
http://tess.elixir-uk.org/materials/material-provided-by-charlotte-soneson
This folder contains material provided by Charlotte Soneson. The following material is included:
Charlotte Soneson @charlotte, charlottesoneson@gmail.com
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Eija_Korpelainen/README.md
http://tess.elixir-uk.org/materials/rna-seq-module-eija-korpelainen
All material concerning RNA-seq data analysis with Chipster
Eija Korpelainen, @eija
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Eija_Korpelainen/RNAseq_data_analysis_with_Chipster_2015/practical_RNAseq_data_analysis_with_Chipster_2015.md
http://tess.elixir-uk.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.
Eija Korpelainen @eija, ekorpelainen@gmail.com
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Jenny_Drnevich/Day2.md
http://tess.elixir-uk.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.
Jenny Drnevich @jenny
Radhika Khetani @radhika
Jessica Kirkpatrick krkptrc2@illinois.edu
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Eija_Korpelainen/RNAseq_data_analysis_with_Chipster_2015/lectures_RNAseq_data_analysis_with_Chipster_2015.md
http://tess.elixir-uk.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.
Eija Korpelainen @eija, ekorpelainen@gmail.com
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://microasp.upsc.se/ngs_trainers/Materials/tree/master/Content/RNA-Seq/Charlotte_Soneson/downstream_analysis_lecture_2015.md
http://tess.elixir-uk.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.
Charlotte Soneson @charlotte, charlottesoneson@gmail.com
Statistical-model, Exploratory-analysis