params.json

{"name":"Urpp tutorials","tagline":"","body":"    \r\n# URPP Tutorials\r\n## URPP Evolution in Action\r\n\r\nStefan Wyder & Heidi Lischer\r\n\r\n\r\n## Linux/Bash shell (3 parts, 3x3h=9h)\r\n\r\n1. [**Basics 1**](https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Tutorial_LinuxPart1.pdf)  \r\n   Folder structure, commands with files&folders, commands with text, piping, (awk)   \r\n   [Hands-on](http://milchmolch.github.io/URPP_Tutorials/LinuxShell/Unix_Part1.html)\r\n2. [**Basics 2**](https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Tutorial_LinuxPart2.pdf)  \r\n   ssh, compression, permission, (bash scripting)  \r\n   [Hands-on](http://milchmolch.github.io/URPP_Tutorials/LinuxShell/Unix_Part2.html)  \r\n3. **Intermediate**  \r\n   - [bash scripting](https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Tutorial_LinuxPart3_HL.pdf) | [Exercises](https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/Exercises_LinuxPart3_HL.pdf)\r\n   - [parallel jobs, awk, regexps](http://milchmolch.github.io/URPP_Tutorials/LinuxShell/Unix_Part3.html) | [Hands-on](https://github.com/milchmolch/URPP_Tutorials/raw/master/LinuxShell/URPP_Hands-on_UnixPart3_SW.pdf)  \r\n\r\n## Next-Generation-Sequencing (4 parts, 4x3h=12h)\r\n\r\n1. [**Introduction**](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part1.pdf)  \r\n   Sequencing Technologies, Quality control (FastQC), SAM/BAM formats, samtools  \r\n   [Hands-on](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Hands-on_NGS_Part1.pdf)  \r\n2. [**Variant Calling**](http://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part2.pdf)  \r\n   Preprocessing BAMs, variant calling example (freebayes), VCF format   \r\n   [Hands-on](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Hands-on_NGS_Part2.pdf)\r\n3. **Variant Calling 2**   \r\n   variant calling (GATK), Variant Effect Prediction   \r\n   [Theory 1](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part3_HL.pdf) | [Theory 2](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_NGS_Part3_SW.pdf) | [Hands-on](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Exercises_NGS_Part3.pdf)\r\n4. **RNA-seq & Making sense of gene lists**  \r\n   Differential expression (edgeR), Gene Ontology Analysis, Gene Set Enrichment Analysis   \r\n   [Theory 1](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_RNAseq_HL.pdf) | [Theory 2](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/URPP_Tutorial_RNAseq_SW.pdf) | [Hands-on 1](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/Exercises_RNAseq_Tutorial_HL.pdf) | [Hands-on 2](https://github.com/milchmolch/URPP_Tutorials/raw/master/NGS/Exercises_RNAseq_Tutorial_SW.pdf)\r\n\r\n## R (3 parts, 2x6.5h+3h=15h)\r\n\r\n[Stefan's website](http://milchmolch.github.io/R_Tutorial/)\r\n\r\n[Heidi's material (pdf documents)]()\r\n\r\n\r\n1. **Introduction into R**  \r\n   Using R as a calculator, variables, subsetting, reading in data, writing functions, apply functions, missing data, plotting (base::plot)\r\n2. **Programming Exercises**  \r\n   Plotting using ggplot2, writing clean code, programming exercises\r\n3. **Programming Exercises 2**  \r\n   Repetition (programming structures, clean coding, project organization)\r\n\r\n\r\n## Introduction to python","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}