timoast.github.io

Tim Stuart ·

September 22, 2016. Put it all together. Clone the repo if you haven’t already:. Git clone https:/ github.com/timoast/dac.git. Install the following packages:. July 12, 2016. I recently analysed some smRNA data for a paper I’m working on. These are my analysis notes. I used previously published data for Brachypodium, from this paper:. First step is to download the data:. Fastq-dump SRR035616.sra $. WGBS Analysis notes - BS-seeker2. March 29, 2016. Step 1: Trim adapters and low quality bases. Altmetric mu...

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Tim Stuart · | timoast.github.io Reviews

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September 22, 2016. Put it all together. Clone the repo if you haven’t already:. Git clone https:/ github.com/timoast/dac.git. Install the following packages:. July 12, 2016. I recently analysed some smRNA data for a paper I’m working on. These are my analysis notes. I used previously published data for Brachypodium, from this paper:. First step is to download the data:. Fastq-dump SRR035616.sra $. WGBS Analysis notes - BS-seeker2. March 29, 2016. Step 1: Trim adapters and low quality bases. Altmetric mu...

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Tim Stuart · | timoast.github.io Reviews

https://timoast.github.io

September 22, 2016. Put it all together. Clone the repo if you haven’t already:. Git clone https:/ github.com/timoast/dac.git. Install the following packages:. July 12, 2016. I recently analysed some smRNA data for a paper I’m working on. These are my analysis notes. I used previously published data for Brachypodium, from this paper:. First step is to download the data:. Fastq-dump SRR035616.sra $. WGBS Analysis notes - BS-seeker2. March 29, 2016. Step 1: Trim adapters and low quality bases. Altmetric mu...

INTERNAL PAGES

timoast.github.io

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About · Tim Stuart

http://timoast.github.io/about

I’m Tim Stuart, a PhD student studying in the Lister lab. At the University of Western Australia. My PhD focuses on the epigenetic regulation of transposable elements in plant genomes.

2

R demo · Tim Stuart

http://timoast.github.io/2016/09/22/r_demo

Put it all together. Clone the repo if you haven’t already:. Git clone https:/ github.com/timoast/dac.git. Install the following packages:. All the following code will assume you are in the directory that holds this file (. In the github repo (ie. Parsed with column specification: # cols( # Accession = col character(), # Coverage = col integer() # ). Also works for gzipped files. Data/mc data.bed.gz". Gzip -dc ./data/mc data.bed.gz". Seq 25 xargs -n 5 echo". Has lots of other useful functions, see dataca...

3

A paper a day · Tim Stuart

http://timoast.github.io/2016/02/23/Papers

A paper a day. In an effort to read more papers this year, I’m going to read a paper (or something paper-like) each day for the remainder of the year, and post each paper below as I go. Galanter JM, Gignoux CR, Oh SS, Torgerson D, Pino-Yanes M, Thakur N, et al. Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures. eLife. doi:10.7554/eLife.20532. Lahmy S, Pontier D, Bies-Etheve N, Laudie M, Feng S, Jobet E, et al. Evidence for ARGONAUTE...

4

Lorne Genome 2016 presentation · Tim Stuart

http://timoast.github.io/2016/02/18/Lorne

Lorne Genome 2016 presentation. This week I presented some recent work at the Lorne Genome conference. It was my first time at Lorne and it’s a fantastic meeting with lots of interesting talks. It was great to see so many people getting interested in transposon biology too! Here are a few links to the work I was presenting:. TEPID TE presence/absence variant discovery software:. Https:/ dx.doi.org/10.6084/m9.figshare.2082757.v1. Http:/ dx.doi.org/10.1101/039511.

5

Code · Tim Stuart

http://timoast.github.io/code

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listerlab.org

Lister Lab - The University of Western Australia

http://www.listerlab.org/people.html

Genetic and epigenomic variation in clonal plants. DNA methylation dynamics in the plant genome. Stem cell epigenomics, epigenome manipulation. Developing gene regulatory circuits for controlling gene expression in plants. Forrest Research Foundation PhD scholar. Genome and epigenome dynamics in brain, bioinformatics. Evolution of DNA methylation systems. Forrest Research Foundation PhD Scholar. Cell type resolution plant epigenomics. Control of DNA methylation patterns in the plant genome.

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timoast.github.io

Tim Stuart ·

September 22, 2016. Put it all together. Clone the repo if you haven’t already:. Git clone https:/ github.com/timoast/dac.git. Install the following packages:. July 12, 2016. I recently analysed some smRNA data for a paper I’m working on. These are my analysis notes. I used previously published data for Brachypodium, from this paper:. First step is to download the data:. Fastq-dump SRR035616.sra $. WGBS Analysis notes - BS-seeker2. March 29, 2016. Step 1: Trim adapters and low quality bases. Altmetric mu...

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