This is a small compilation of links to get started and familiar with git, github, command-line and R.
Learn git with exercises and a console in a browser: try.github.io >> does not take long and is fun.
Happy git with R is a great manual to learn git for RStudio, includes tipps and tricks and more ressources.
SOS for git along the line oh shit, I did so and so, how can I make it right again?: ohshitgit.com.
If you work with sensitive (human) data (e.g. anything that contains an identifier of an individual), you occasionally want to share that data. The most straightforward way to do so is to send them by email (and yes - we are all guilty of that!). The problem arises, if the data get into wrong hands. Let's say you send the email accidentally to the wrong person. Or worse, without your knowledge, the email gets into the wrong hands.
The good news is, that there is a secure & handy solution for this. But let's first have a look at some other solutions.
I hereby claim:
To claim this, I am signing this object:
Below are instructions how to get streaming, recording or webinars working.
Livestreaming of a meetup is a great opportunity for people who cannot be present otherwise (e.g. other responsibilities or because they are located elsewhere). However, unless expensive technical equipment is used and lots of social media interaction happens, the quality of a livestream will not replace the actual physical meetup experience.
| # satRdays Cardiff 2018 | |
| This is a brief write-up of my [satRdays Cardiff](http://cardiff2018.satrdays.org/) experience. | |
| First - what is a [**satRday**](http://satrdays.org/)? | |
| It is an awesome concept: attending an **R conference** organised by a **local RUG** on a **Saturday**. | |
| The [programme](http://cardiff2018.satrdays.org/#programme) in Cardiff had parallel sessions - tough decision-making to pick between promising talks! |
Below are instructions on how to extract single SNP data from large genetic datasets.
*.map, *.ped or *.bed, *.bim,*.fam)*.gen or its binary version: *.bgen)*.vcf.gz)More on genetic data file formats here.
| Here are some extra (unpolished) code snippets for the R-package `biomaRt` that came up during the writing of the [blogpost](https://sinarueeger.github.io/content/post/2018-07-27-GWAS-annotation). | |
| ## Extract all SNPs for a particular genomic region | |
| ```{r, get-snp-info-pos-chr, include = TRUE, cache=TRUE, eval=FALSE} | |
| library(biomaRt) | |
| ## select mart | |
| snpmart = useMart(biomart = "ENSEMBL_MART_SNP", dataset="hsapiens_snp") |
| library(readbitmap) | |
| library(gganimate) | |
| library(dplyr) | |
| library(ggplot2) | |
| b1 <- read.bitmap("~/Documents/rladies.png") | |
| b2 <- read.bitmap("~/Documents/sydney.png") | |
| x1 <- 1 - b1[,,1] | |
| x2 <- 1 - b2[,,1] | |
| # plot(raster::raster(x1)) # check | |
| # plot(raster::raster(x2)) # check |
| --- | |
| title: "icons" | |
| output: | |
| pdf_document: | |
| toc: true | |
| latex_engine: pdflatex | |
| dev: cairo_pdf | |
| monofont: Menlo | |
| --- |
Helpful links for developing R packages