Bioinformatics
Interesting Bioinformatics Articles
Following is a collection of articles which I feel every Bioinformatician must be aware of. I will keep updating this list from time to time - 1. All biology is computational biology 2. Core services: Reward bioinformaticians 3. Importance of stupidity in scientific research
Screen command in UNIX
Screen is a very useful command to have in your toolbox if you frequently use interactive sessions on your supercomputer logged in through a VPN. A VPN typically has a time limit, and you may get disconnected from it without any warning when you have poor internet connection. Screen program
Types of models in DESeq2
There are 2 major types of regression models one can specify in DESeq2 to explore the raw count matrices from an RNA-seq experiment - * Mean-reference model for Factors * Regression model for Covariates Mean-reference model for Factors - Factors typically represent categorical variable such as Gender, Ethnicity, Race etc. The mean-reference
Steps in DESeq function
For any RNA-seq data analysis project, one would most probably end up using the R package DESeq2. The function 'DESeq' is the main function that is called to obtain the differentially expressed genes. But what exactly does this function do? In short, DESeq function combines the following 3 steps -
Normalize Counts Matrix in DESeq2
I followed Josh Starmer's YouTube video on how DESeq2 normalizes the raw counts matrix, and attempted to reproduce the steps in R. This normalization procedure accounts for both the library size (total no. of reads in each sample) as well as the library composition (enables us to compare between different
Advice for Bioinformaticians
Keith Bradnam has an excellent series of interviews with 39 notable Bioinformaticians at this link. Anyone interested in the field of Bioinformatics should check it out! Following is a summary of the advice from interviewees - 1. There is always something new to learn in Bioinformatics everyday. It is an
Getting Started With Bioinformatics
When I first heard about the field of Bioinformatics, I thought about how cool it would be to work in this field. The idea of analyzing sequencing data using computers fascinated me. I was not good at running microbiology experiments anyway, and the scope for variability with performing such experiments
Selecting Genes from a DEG List
Let's consider the scenario where we would like to select genes from a differential expression analysis list that show at least 30% increase or 30% decrease in expression. This can be confusing at first if you attempt it based on the log fold change values. So let's look into this
Deploying your shiny app on shinyapps.io
Following are the commands you would require to deploy your shiny app successfully onto https://shinyapps.io/ for the whole world to use -
rsconnect::setAccountInfo(name='
stringsAsFactors trouble in R
Recently, I was reading a counts matrix in R - > counts <- read.table("htseq_counts_matrix.txt") > head(counts) Pool5_RNAseq_12_S33_L006 Pool5_RNAseq_19_S34_L006 ENSMUSG00000000001 4676 2314 ENSMUSG00000000003 0 0 ENSMUSG00000000028 558 172 ENSMUSG00000000031 25272 6334 ENSMUSG00000000037 2
