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Commits (3)
.Rproj.user
.Rhistory
.RData
.Ruserdata
intro-to-bioinf.Rproj
.DS_Store
---
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
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.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;
}
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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
---
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")
```
---
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)
```