Create a directory with multiple sub-directories mkdir -p output_folder/{raw_data,temp_data,result,log_folder} Go to specific line number using vi vi +14 filename This will open the file at lin...
Creating a static webpage
Getting Started I used the Jekyll chirpy theme for this webpage. Follow the following steps to create your own webpage. Steps: First go to the Chirpy github page. Click on the Chirpy star...
Bar plot based on proportion for each individual group
Lets load the dataset import pandas as pd import seaborn as sns df = sns.load_dataset('tips') df.head() total_bill tip sex smoker day time size 0 16.99 1.01 Female No Sun Dinner 2 1 10.34 1.66 M...
Divide pandas dataframe into bins
Dividing pandas dataframe into bins using qcut and cut Lets use a sample dataframe df = sns.load_dataset('iris') df.head() Lets say we want to divide the dataframe into 5 bins based on the peta...
Biological Data Resources
Human protein Atlas IntAct Cistrome Expression Atlas ARCHS4 (RNA Seq) GTEx Metascape Depmap portal cBioPortal
Generate Frequency count table and motif logo from given fasta sequences
To generate a motif logo first we need to create a count table for the nucleotide bases from fasta sequences and then information matrix to plot motif logo Create count table from fasta sequence ...
Single letter representation of ambiguous nucleotide
Although DNA sequences are represented by four nucleotide bases (A,T,G,C) they can be represented by alternate letters based on different scenario. One of the example would be sequencing data, wher...
Histone Modifications and chromatin states
Histone modification play an important role in gene regulation and based on different histon modification signatures, it can be used to annotate different chromatin states. The following picture pr...
Calculating phyloP conservation score over certain genomic region
phyloP scores can be used to identify the evolionary rate of genomic sequences. Positive score represents slower evolution or more conserved sequence and negative score represents faster evolution....
Create Genome Index file to map sequencing data
There are several tools available map sequencing data to the reference genome. And for all of the tools index files needs to be generated first. Here are some of the tools and the syntax used to ge...