Publications by Vennila Ramasubramanian
Document
Default working directory Open up this .Rmd file in RStudio. In the code chunk below type getwd() and run it. “wd” means “working directory”, or where R will currently save files if you tell it to save anything. # Get the current working directory getwd() ## [1] "/Users/vennilaram/Downloads/compbio" Copy and paste the current wd in the co...
1708 sym R (335 sym/4 pcs)
Creating Pairwise Alignments and an MSA for Shroom Family
A complete bioinformatics workflow in R By: Nathan L. Brouwer “Worked example: Building a phylogeny in R” Introduction #Phylogenies can be used to show when genes or species diverged due to evolution,which genes or species are more similar or more different to each other, what a common ancestor is for 2 genes or species, and which genes or ...
838 sym R (16374 sym/61 pcs) 1 img
Working Directory
Default working directory Open up this .Rmd file in RStudio. In the code chunk below type getwd() and run it. “wd” means “working directory”, or where R will currently save files if you tell it to save anything. # Get the current working directory getwd() ## [1] "/Users/vennilaram/Downloads/compbio" Copy and paste the current wd in the co...
1708 sym R (325 sym/4 pcs)
Downloading DNA sequences as FASTA files in R
This is a modification of “DNA Sequence Statistics” from Avril Coghlan’s A little book of R for bioinformatics.. Most of the text and code was originally written by Dr. Coghlan and distributed under the Creative Commons 3.0 license. NOTE: There is some redundancy in this current draft that needs to be eliminated. Functions library() help...
12658 sym R (2160 sym/40 pcs)
Adjusting dotplot setting in R to investigate sequence repeats in Shroom
Add the necessary code to make this script function. Preliminaries Load packages library(seqinr) library(rentrez) library(compbio4all) library(Biostrings) ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ## ...
1193 sym R (6215 sym/37 pcs) 5 img
Investigating BHLHE41 for the presence of repeats
Preliminaries Load packages library(seqinr) library(rentrez) library(compbio4all) library(Biostrings) ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ## clusterApply, clusterApplyLB, clusterCall, clusterEv...
927 sym R (6047 sym/35 pcs) 5 img
Pie graphs from 'Genomics is failing on diversity' by Popejoy and Fullerton
Introduction This data shows the divesity breakdown of participants in GWAS in both 2009 and 2016. The 2009 data was collected by A.C. Need and D.B. Goldstein, and the 2016 data was collected by Alice B. Popejoy and Stephanie M. Fullerton. It was collected by analysis of sample descriptions in the GWAS Catalog. The process was repeated in 2016 to...
760 sym R (1044 sym/3 pcs) 1 img
Testing Google Sheets Access
The goal of this exercise is to make you familiar with how to download data from Google Sheets and to briefly review some key concepts R functions and coding concepts. We’ll do the following things download a list of RefSeq accessions from a Google sheet remove the NAs using na.omit() select out all but one isoform using duplicated() Packages...
865 sym R (2756 sym/25 pcs)