How to create a 3D pie chart in R
The Pie Chart, represented in the circular chart symbol, is easy to understand complex data. Each section of the circle shows the data value...
Sanjay Singh
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KEGG Sequence Downloader : retrieve gene sequences in Fasta format from KEGG database
I wanted to download the gene sequence of tobacco from NCBI . Since NCBI also contains the isoform and some other unwanted genes, therefore ...
Easiest way to find number of cluster in gene expression data
Gene clustering is a common method to find the groups of the gene with similar expression patterns. However, it is not always easy to decid...
Easiest way to calculate Ka Ks ratio and divergence time
The Ka/Ks ratio is used to estimate the nature of evolution among neutral, purifying selection and beneficial mutations acting on a set of h...
Draw a heatmap with Custom Symbol in Cell
Heatmap is a good way to save some space when you want to compose a figure with lots of panels. I got some gene expression data which were s...
How to add function descriptions to FASTA sequences
Short descriptions in fasta sequence help us to quickly gain insight into important information about a sequence. Automatic assignment of Hu...
How to rename fasta headers according to a matching name list
FaBox has several utilities to manipulate the FASTA sequence. I wanted to replace the FASTA header with the new header or description which...
How to get gene expression value from Arrayexpress
ArrayExpress has a wonderful R package for data search, download and analysis but it doesn't always work in perfection. Therefore it alw...
Easiest way to download multiple sequences from NCBI
NCBI and me have shared several tricks to download large set of sequence from database HERE and HERE , respectively. In this post. I am goi...
How to perform parallel BLAST
BLAST can be time-consuming especially when it includes a large number of the query sequence. Therefore, parallel BLAST can be useful. This...
Cheat Sheet to Install and work with R on Ubuntu
Tips and tricks to Install and work with R on Ubuntu Run these commands in terminal #Update and Install R sudo apt-get update sudo apt-get i...
Get multiple strings from a file and replace them in another file with AWK
Get multiple strings from a file and replace them in another file I have multiple strings (old strings) and their sustitution (new strings) ...
Examples For Sed Linux Command In Text Manipulation and File Handling
Click on red strip to expand it 1. Replace all occurrence 1. Replace all occurrence Ram in Inputfile with Shyam and save the re...
How to compare multiple sets using UpsetR
Why UpSet Everyday I face the problems that need to understand the relationships between sets. Ven diagram always a great job if the number ...
How to make a group bar graph with error bars and split y axis
I would like to draw a group bar graph with error bars and split y axis to show both smaller and larger values in same plot. Although plotri...
How to make a Heatmap with multiple annotation
I was interested to make a heatmap with multiple annotation with least interference. It will create an heatmap with multiple annotation such...
How to download expression data set from NCBI GEO
NCBI has provided a wonderful tool GEO2R to do analysis of microarray data sets but sometime I need the normalized data sets to check the e...
How to perform Non-metric multidimensional scaling (NMDS) analysis
Requirements We need R libraries vegan , ggplot2 , extrafont to run this script. R scripts For complete result of analysis and raw file, pl...
Easiest Way to Download All Sra Samples or Multi Experiment file from NCBI SRA database- II
Previously I shared a easy way to download the data files from NCBI SRA database . Although it took only wget to download the data files bu...
How To Predict CRISPR-Cas9 target site in R
Although there are several online bioinformatics tools to predict the target site for CRISPR-Cas9 but I was looking for a offline solution....