Big Picture
Study Guide - Beginners
Study Guide - Intermediate
Tutorials on RNAseq Analysis
Tutorials on Genome Assembly
Bioinformatics Algorithms
Expert Membership Content - July 2020
Heatmaps for gene expression data
Do you like to draw beautiful heatmaps for your gene expression data? Here I show examples from three libraries - base R, ggplot and pheatmap - Check here.
Do you like to draw beautiful heatmaps for your gene expression data? Here I show examples from three libraries - base R, ggplot and pheatmap - Check here.
Cleaned up tutorial on R plots and gviz
Check here.
Check here.
Tutorial on R-shiny
Check here.
Check here.
Expert Membership Content - May-June 2020
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ggplot Bonanza
This month, we are looking into four topics - (i) Combining multiple plots using libraries like cowplot, grid or patchwork, (ii) Animated ggplots, (iii) R-shiny apps, (iv) Drawing phylogenetic trees using ggplot.
This month, we are looking into four topics - (i) Combining multiple plots using libraries like cowplot, grid or patchwork, (ii) Animated ggplots, (iii) R-shiny apps, (iv) Drawing phylogenetic trees using ggplot.
Combining multiple plots using libraries like cowplot, grid or patchwork
Our New/Revised Tutorials - Biology
Our New/Revised Tutorials - High School
Minimalist R for Fun Math and Biology
Move Seamlessly from Excel to R
Data Visualization for Biology in R
Our New/Revised Tutorials - High School
Expert Membership Content - Mar 2020
Tracking the COVID-19 Pandemic
Expert Membership Content - Nov 20, 2019
R for Proteomics
If you are performing proteomics in R for the first time, the best places to start are listed in this tutorial along with description of the common packages. We are working on a detailed proteomics tutorial, and this is the first step.
Continue reading here...
If you are performing proteomics in R for the first time, the best places to start are listed in this tutorial along with description of the common packages. We are working on a detailed proteomics tutorial, and this is the first step.
Continue reading here...
Expert Membership Contents - Sept 2019
Thousand Dollar Server for Biology
This is the first draft of a manual I prepared to help biologist set up lab computing infrastructure for NGS data analysis. Our organization has been using this operating system set up for several years. It allows creating multiple virtual machines customized for users or tasks. Also, it makes the installation of bioinformatics programs is rather straightforward. ((Link for Tutorial).
This is the first draft of a manual I prepared to help biologist set up lab computing infrastructure for NGS data analysis. Our organization has been using this operating system set up for several years. It allows creating multiple virtual machines customized for users or tasks. Also, it makes the installation of bioinformatics programs is rather straightforward. ((Link for Tutorial).
Expert Membership Content - Aug 2 - 15, 2019
Thousand Dollar Server for Biology
Over the next two weeks, we plan to work actively on the "thousand dollar server" tutorial.
Over the next two weeks, we plan to work actively on the "thousand dollar server" tutorial.
Expert Membership Content - July 26- Aug 1, 2019
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Introductory: Condensed Biopython Tutorial
Continue reading here...
Continue reading here...
Intermediate: Metaprogramming in R, Where Code Writes Code
One interesting aspect of R is that you can create new functions in a compact way. We demonstrate that with an example, where we create simple functions like sum1(N)=1+2+3+...+N, sum2(N)=1^2+2^2+....N^2 and so on.
Continue reading here...
One interesting aspect of R is that you can create new functions in a compact way. We demonstrate that with an example, where we create simple functions like sum1(N)=1+2+3+...+N, sum2(N)=1^2+2^2+....N^2 and so on.
Continue reading here...
Advanced: Git Tricks to be Dangerous
In this tutorial, we go behind the scene to see what the commands like "git add" and "git commit" do. The main lesson is that git stores every version of your entire file in a separate tree link maintained by three "objects". Therefore, if you frequently commit minor changes in a large file, your git folder will grow rapidly, and your git project will take time to download.
Rare situations arise, when you may have submitted sensitive or embarrassing information in the git folder. It is possible to clean up the public git history in such scenarios as described later in this tutorial.
Continue reading here...Expert Membership Content - July 19-25, 2019
Python for Biology
This week, instead of posting materials here, I worked actively on our Python tutorial. This greatly improved version will be accessible to our Expert Members.
This week, instead of posting materials here, I worked actively on our Python tutorial. This greatly improved version will be accessible to our Expert Members.
Expert Membership Content - July 12-18, 2019
Introductory: Python for Beginners
Many students learn Python, but do not know how to convert their ideas into Python. Here we will explain a general problem-solving strategy based on the following problem.
Continue reading here...
Many students learn Python, but do not know how to convert their ideas into Python. Here we will explain a general problem-solving strategy based on the following problem.
Continue reading here...
Advanced: Rules of the Genome - 2
Based on review of the books "Origin of Genome Architecture" by Michael Lynch and "Molecular and Genome Evolution", we write a number of patterns seen in the sequenced genomes.
Continue reading here...
Based on review of the books "Origin of Genome Architecture" by Michael Lynch and "Molecular and Genome Evolution", we write a number of patterns seen in the sequenced genomes.
Continue reading here...
Expert Membership Content - July 5-11, 2019
Introductory: Genetics of Color Blindness
A number of opsin genes assist us in seeing colors. In a recent review titled "Genetic Variation, Comparative Genomics, and the Diagnosis of Disease", Evan Eichlar described mutations in those genes leading to color blindness. Now that you know how to solve the "hardest easy problem", you can extract the sequences of those gene from genome and see what happens in the presence of a mutation.
Continue reading here...
A number of opsin genes assist us in seeing colors. In a recent review titled "Genetic Variation, Comparative Genomics, and the Diagnosis of Disease", Evan Eichlar described mutations in those genes leading to color blindness. Now that you know how to solve the "hardest easy problem", you can extract the sequences of those gene from genome and see what happens in the presence of a mutation.
Continue reading here...
Intermediate: Visualization of Arabidopsis Data using Gviz
An expert member requested for an example on visualization of genomic data from Arabidopsis using Bioconductor. Here it is. Continue reading here...
An expert member requested for an example on visualization of genomic data from Arabidopsis using Bioconductor. Here it is. Continue reading here...
Advanced: Rules of the Genome - 1
Based on review of the books "Origin of Genome Architecture" by Michael Lynch and "Molecular and Genome Evolution", we write a number of patterns seen in the sequenced genomes. Continue reading here...
Based on review of the books "Origin of Genome Architecture" by Michael Lynch and "Molecular and Genome Evolution", we write a number of patterns seen in the sequenced genomes. Continue reading here...
Expert Membership Content - June 28-July 4, 2019
Join Expert Membership: here
Introductory: The Hardest Easy Problem in Bioinformatics
Here we solve the following problem - "extract the coding sequence of a multi-exon gene from the human (or other large eukaryotic) genome and translate it to find the protein sequence."
Experienced bioinformaticians can answer the question without blinking, but those biologists learning bioinformatics for the first time find it challenging. Continue reading here...
Here we solve the following problem - "extract the coding sequence of a multi-exon gene from the human (or other large eukaryotic) genome and translate it to find the protein sequence."
Experienced bioinformaticians can answer the question without blinking, but those biologists learning bioinformatics for the first time find it challenging. Continue reading here...
Intermediate: Three Helpful ggplot Tricks
(i) How do we annotate a subset of genes (or points) in the plot?
(ii) How do we change the default color scheme?
(iii) How do we add a small subplot within our plot?
(i) How do we annotate a subset of genes (or points) in the plot?
(ii) How do we change the default color scheme?
(iii) How do we add a small subplot within our plot?
Advanced: Recent Advanced in the Genome Assembly Field
The genome assembly field continues to be highly active, and the researchers are coming up with algorithms making significant speed improvements. This commentary presents a number of recent advances and also several useful recourses providing review of the field. Continue reading here...
The genome assembly field continues to be highly active, and the researchers are coming up with algorithms making significant speed improvements. This commentary presents a number of recent advances and also several useful recourses providing review of the field. Continue reading here...
Expert Membership Content - June 21-27, 2019
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Introductory: Which Tetramer is the Least Frequent in the E. coli Genome?
Although this exercise is simple, it illustrates several interesting concepts from biology (biochemistry), bioinformatics and coding. Continue reading here...
Although this exercise is simple, it illustrates several interesting concepts from biology (biochemistry), bioinformatics and coding. Continue reading here...
Intermediate: Comparison of Two E. coli Genomes using MUMMER and R
Here we demonstrate genome comparison using Mummer and visualization of comparison results using R. Continue reading here..
Here we demonstrate genome comparison using Mummer and visualization of comparison results using R. Continue reading here..
Advanced: $1000 Server for NGS Biology Labs
We often hear about sequencing the human genome for $1000, but the computational costs have bigger factors in today's biology. In a series of posts, we show an inexpensive server system that can benefit the biologists. Continue reading here..
We often hear about sequencing the human genome for $1000, but the computational costs have bigger factors in today's biology. In a series of posts, we show an inexpensive server system that can benefit the biologists. Continue reading here..
Welcome - Nov. 16, 2016
We are relaunching the site after months of work. The following email had been sent to all researchers, who registered at the website. Continue reading here..
