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- 2010
- Advanced RNA-Seq and ChiP-Seq data analysis
Advanced RNA-Seq and ChiP-Seq data analysis
EMBL Heidelberg, Germany
2010-06-07 ~ 2010-06-09
Instructors
- Martin Morgan
- Patrick Aboyoun
- Simon Anders
- Nico Delhomme
- Petra Schwalie
- Charles Girardot
- Paul Bertone
- Wolfgang Huber
Description
The course covers data analysis of ChIP-Seq and RNA-Seq experiments including Alignment, data handling and visualisation, region identification, differential expression, data quality assessment, integrative bioinformatic and statistical analysis, using R/Bioconductor as well as other open source software tools.
Materials
- R / Bioconductor Packages for Short Read Analysis
- Short Read Alignment
- ShortRead and Rsamtools for Input and Quality Assessment
- IRanges, GenomicRanges, and Biostrings
- GenomicFeatures and BSgenome
- Differential expression analysis for sequencing count data
- ChIP-seq data analysis with SWEMBL
- MACS, CisGenome, SISSRs and other peak calling algorithms
- Sensitivity, Specificity, ROC, Multiple testing, and Independent filtering
- Hilbert curves
- Practical 1: Reading and Manipulating Short Reads
- Practical 3: A ChIP-Seq Workflow
- Practical 4: Finding Structural Variants in Short Read, Paired-end Sequence Data with R and Bioconductor
- EMBL2010_0.0.11.tar.gz package - An R package
containing slides and exercise material. Download, then install in R using
install.packages("EMBL2010_0.0.11.tar.gz", repos=NULL, type="source")