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January 12, 2017. January 12, 2017. This is your very first post. Click the Edit link to modify or delete it, or start a new post. If you like, use this post to tell readers why you started this blog and what you plan to do with it. Create a free website or blog at WordPress.com.
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January 12, 2017. January 12, 2017. This is your very first post. Click the Edit link to modify or delete it, or start a new post. If you like, use this post to tell readers why you started this blog and what you plan to do with it. Leave a Reply Cancel reply. Enter your comment here. Fill in your details below or click an icon to log in:. Address never made public). You are commenting using your WordPress.com account. ( Log Out. You are commenting using your Twitter account. ( Log Out.
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January 12, 2017. January 12, 2017. This is your very first post. Click the Edit link to modify or delete it, or start a new post. If you like, use this post to tell readers why you started this blog and what you plan to do with it. Create a free website or blog at WordPress.com.
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Publications
https://arundurvasula.wordpress.com/publications
Hoffman PJ*, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J. (2016) ANGSD-wrapper: utilities for analyzing next generation sequencing data. Molecular Ecology Resources. Beissinger TM, Wang L, Crosby K, Durvasula A. Hufford MH,Ross-Ibarra J. (2016). Recent demography drives changes in linked selection across the maize genome. Nature Plants. Haplotype networks in R. The effect of excess reads and uneven coverage on viral sequence assembly. Interpreting Tajima’s D. PCA with ANGSD and ngsCovar.
March 2014
https://arundurvasula.wordpress.com/2014/03
Gene Ontology and Object Oriented Programming. March 31, 2014. The Gene Ontology (GO, http:/ www.geneontology.org. In object oriented programming, inheritance promotes code reuse without duplication. The way this works (briefly) is, a base class is created containing methods and variables that classes could inherit from it. For example, if you were modeling vehicles, you could have a Vehicle class, which contains methods like. Etc and variables like. As well as the variables like. The point is, not all o...
Haplotype networks in R
https://arundurvasula.wordpress.com/2016/02/24/haplotype-networks-in-r/comment-page-1
Haplotype networks in R. February 24, 2016. March 19, 2016. Haplotype networks are pretty useful for genomic analyses, especially when you’re looking at phylogeography ( Shannon et al 2015. Or if you’re looking at a region of special interest ( Huerta-Sánchez et al 2014. A quick google search will turn up a number of blog posts that tell you how to use pegas. To use it, you should supply a vcf file (gzipped or not is fine), an output filename, and a chromosome of interest:. This script will go through th...
Haplotype networks in R
https://arundurvasula.wordpress.com/2016/02/24/haplotype-networks-in-r
Haplotype networks in R. February 24, 2016. March 19, 2016. Haplotype networks are pretty useful for genomic analyses, especially when you’re looking at phylogeography ( Shannon et al 2015. Or if you’re looking at a region of special interest ( Huerta-Sánchez et al 2014. A quick google search will turn up a number of blog posts that tell you how to use pegas. To use it, you should supply a vcf file (gzipped or not is fine), an output filename, and a chromosome of interest:. This script will go through th...
Tutorials and Topics
https://arundurvasula.wordpress.com/tutorials-and-topics
Here’s a list of tutorials and topic reviews on this blog. PCA with samtools and plink. PCA with ANGSD and ngsCovar. Leave a Reply Cancel reply. Enter your comment here. Fill in your details below or click an icon to log in:. Address never made public). You are commenting using your WordPress.com account. ( Log Out. You are commenting using your Twitter account. ( Log Out. You are commenting using your Facebook account. ( Log Out. You are commenting using your Google account. ( Log Out.
April 2014
https://arundurvasula.wordpress.com/2014/04
Remote IPython notebook with Raspberry Pi. April 1, 2014. December 13, 2015. It recently stuck me that I’d really like to do some data analysis on my iPhone. This is pretty impractical because it’s a tiny screen and the keyboard often autocorrects and capitalizes things I don’t want it to, but I still wanted to do it because 1) I can, and 2) why not? To do this, I connected my Raspberry Pi. To set up the static IP, I basically followed these directions. Installing IPython and friends. C = get config().
May 2014
https://arundurvasula.wordpress.com/2014/05
Using synthetic lethality for targeted cell death. May 13, 2014. This type of interaction can be taken advantage of when cell death is desired, namely, cancer cell death. Scientists have observed that most cancer cells have mutations in cohesin related genes, which are genes that create proteins that oversee how chromosomes separate during cell replication. And a nematode worm (. These organisms have very similar replication systems, and as the authors hypothesized, would be representative of how human s...
April 2015
https://arundurvasula.wordpress.com/2015/04
The effect of excess reads and uneven coverage on viral sequence assembly. April 29, 2015. April 29, 2015. Tl;dr: it makes it harder. Use IDBA UD for assembly. Code: https:/ github.com/arundurvasula/coverage-depth-assembly. One of the coolest results of RNA biology has been the ability to reconstruct full viral genomes from the sequencing of siRNAs found in eukaryotes. The Wu et. al. 2010 paper in PNAS ( http:/ www.pnas.org/content/107/4/1606.full.pdf. Coverage: 50x. Method: subsampling. As you can see f...
February 2016
https://arundurvasula.wordpress.com/2016/02
Haplotype networks in R. February 24, 2016. March 19, 2016. Haplotype networks are pretty useful for genomic analyses, especially when you’re looking at phylogeography ( Shannon et al 2015. Or if you’re looking at a region of special interest ( Huerta-Sánchez et al 2014. A quick google search will turn up a number of blog posts that tell you how to use pegas. To use it, you should supply a vcf file (gzipped or not is fine), an output filename, and a chromosome of interest:. This script will go through th...
PCA with ANGSD and ngsCovar
https://arundurvasula.wordpress.com/2015/02/08/pca-with-angsd-and-ngscovar
PCA with ANGSD and ngsCovar. February 8, 2015. February 8, 2015. As a follow up to the last post ( PCA with samtools and plink. I’m going to go over how to do PCA using genotype likelihoods from ANGSD and with ngsCovar. This method isn’t integrated in to angsd-wrapper. Yet, but we are looking to add it. The documentation is a little light for ngsCovar, but there is a tutorial here. Shout out to Peter Fields for linking me to that). Gunzip all.test.geno.gz. Then, following the graphing part of the tutorial.
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