.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+intro-to-bioinf.Rproj
+.DS_Store
+

00_introduction/introduction.Rmd

+---
+title: 'Introduction to Bioinformatics with R and Bioconductor'
+author: "Thomas Schwarzl"
+date: "26/3/2019"
+output:
+    slidy_presentation: 
+        theme: simplex
+        css: styles.css
+header-includes:
+- \newcommand{\bcenter}{\begin{center}}
+- \newcommand{\ecenter}{\end{center}}
+logo : img/embl_logo_small.png
+biglogo : img/embl_logo.png
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = FALSE)
+```
+
+## Welcome
+
+<div class="midcenter" style="margin-left:-300px; margin-top:-200px;"><img src="img/Wikipedia_welcome_committee_topicon_graphic.PNG"  width="600"></img></div>
+
+## About me - Thomas Schwarzl
+
+<img src="img/Thomas_Schwarzl.jpeg" height=150></img>
+
+Positions                                 |  Locations
+----------------------------------------- | -----------------------------
+Chemical enigneer                         | HTL17 Vienna (Austria)
+BSc in Bioinformatics                     | FH Hagenberg (Austria) 
+PhD in Bioinformatics and Systems Biology | UCD Dublin (Ireland)
+PostDoc in Hentze and Huber lab           | EMBL Heidelberg (Germany)
+Staff Scientist Hentze and Huber lab      | EMBL Heidelberg (Germany)
+
+
+## About the (other) trainers
+<div><img src="img/FlorianHuber.jpg" class="portrait" />
+Florian Huber<br />
+<span class="subtext">EIPOD PostDoc in Typas and Beltrao groups</span></div>
+<br class="clear" />
+<div><img src="img/TheaVanRossum.jpg" class="portrait" />Thea Van Rossum<br /><span class="subtext">PostDoc in Bork group</span></div>
+<br class="clear" />
+<div><img src="img/BerndKlaus.png" class="portrait" />(Bernd Klaus)<br/>
+<span class="subtext">previously Biostatistician at EMBL </span></div>
+<br class="clear" />
+
+## About the teaching assistents
+
+<div><img src="img/CharlesGirardot.jpeg" class="portrait" />Charles Girardot<br /><span class="subtext">Head of Genome Biology Computational Support group</span></div>
+<br class="clear" />
+<div><img src="img/SudeepSahadevan.jpeg" class="portrait" />Sudeep Sahadevan<br /><span class="subtext">Bioinformatics Engineer in Hentze group</span></div>
+<br class="clear" />
+
+## About the course organizers
+
+<div><img src="img/ElisabethZielonka.jpg" class="portrait" />Elisabeth Zielonka<br /><span class="subtext">Scientific Organiser</span></div>
+<br class="clear" />
+
+<div><img src="img/Luca-Ruse.jpg" class="portrait" />George Luca-Ruse<br /><span class="subtext">Course Organiser</span></div>
+<br class="clear" />
+
+## What is bioinformatics
+
+> - Data preprocessing
+> - Exploration
+> - Statistical analysis
+> - Visualisation
+
+## Course program
+
+> - *Monday* - R refresher / Data processing
+> - *Tuesday* - Data processing Visualisation and Exploration
+> - *Wednesday* - Hypothesis testing and Statistical analyses
+> - *Thursday* - Applied analyses
+
+## Exact program and house rules
+
+ --> to Elli 

00_introduction/styles.css

+.title-slide {
+    background-image: url('img/embl_background.jpg');
+}
+
+.portrait {
+    float: left;
+    height: 150px;
+    margin: 0px 15px 15px 0px;
+}
+.midcenter {
+    position: fixed;
+    top: 50%;
+    left: 50%;
+}
+
+.clear {
+    clear:both;
+}
+
+.center {
+    text-align: center;
+}
+
+.fleft {
+    float: left; margin: 0px 15px 15px 0px;
+}
+
+#nextsteps {
+   color: blue;
+}
+
+.emphasized {
+   font-size: 1.2em;
+}
+
+.subtext {
+    font-size: 0.7em;
+}

07_introduction_to_bioconductor/bioconductor_cache/slidy/__packages

+base
+BiocStyle
+BioC2016Introduction
+BiocGenerics
+S4Vectors
+IRanges
+GenomeInfoDb
+GenomicRanges
+Biobase
+matrixStats
+BiocParallel
+DelayedArray
+SummarizedExperiment
+airway
+XVector
+Biostrings
+rtracklayer
+BSgenome
+BSgenome.Hsapiens.UCSC.hg19
+Rsamtools
+VariantAnnotation
+AnnotationDbi
+GenomicFeatures
+TxDb.Hsapiens.UCSC.hg19.knownGene

10_annotation/annotation.Rmd

+---
+title: "Annotation"
+author: "Thomas Schwarzl"
+date: "29/3/2019"
+output: html_document
+---
+
+```{r}
+suppressPackageStartupMessages({
+    library(Organism.dplyr) 
+    library(TxDb.Hsapiens.UCSC.hg38.knownGene)
+})
+```
+
+
+```{r}
+supportedOrganisms() %>% filter(organism == "Homo sapiens")
+```
+
+```{r}
+src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")
+```
+
+

data/RNASeq-Airway.Rmd

+---
+title: "RNASeq-Airway"
+author: "Thomas Schwarzl"
+date: "28/3/2019"
+output: BioCStyle::html_document
+---
+
+```{r}
+if (!requireNamespace("BiocManager")) install.packages("BiocManager")
+BiocManager::install(c("airway"))
+```
+
+```{r}
+list.of.packages <- c("ggplot2", "Rcpp")
+new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
+if(length(new.packages)) install.packages(new.packages)
+```