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View hpcc_job_submission.py
#!/usr/bin/python3 env
# -*- coding: utf-8 -*-
"""Qsub command generator
Author: Arup Ghosh
Creation date: 17/07/2019
last modified: 18/07/2019
Email: arupneo2 [at] gmail.com
"""
import glob
View topGO.run.R
#Pathways for scRNA
library(dplyr)
library(Matrix)
library(MASS)
library(topGO)
library(xtable)
source("topGO.script.R")
#Run the topGOterm dunctiom
View topGO.script.R
#' Find Variable genes using a negative binomial null model
#' cut.quantile - quantile ceiling on max counts
# source: https://github.com/karthikshekhar/CellTypeMIMB
NB.var.genes <- function(
object = object,
cells.use=NULL,
min.cells = 200,
do.idents=NULL,
genes.use = NULL,
do.plot=TRUE,
View Display_protein_sequence_like_Uniprot.php
# PHP function to display protein sequence in Uniprot like format
# Author Arup Ghosh
# Use $len = 60
function processSeq($str,$len){
$arr = str_split($str,$len);
$i=1;
// The code will be improved in future revisions
foreach($arr as $bit){
$k10=str_split($bit,10);
View README.txt
Contents of : ftp://ussd-ftp.illumina.com/README.txt
Illumina iGenomes
The iGenomes are a collection of sequence and annotation files for commonly
analyzed genomes. Each iGenome contains data for one species, downloaded from
one source (UCSC, NCBI, or Ensembl), for one genomic build.
@arupgsh
arupgsh / pubmed_search.py
Created Feb 21, 2018
Search PubMed database and return PMIDs.
View pubmed_search.py
from Bio import Entrez
Entrez.email = "yourmail@gmail.com"
handle = Entrez.esearch(db="pubmed", term="cancer", retmax="10", sort="relevance", retmode="xml")
records = Entrez.read(handle)
print records["IdList"]
@arupgsh
arupgsh / pub_med.py
Created Feb 21, 2018 — forked from ehazlett/pub_med.py
Search PubMed with BioPython
View pub_med.py
#!/usr/bin/env python
# numpy and biopython are required -- pip install numpy biopython
from Bio import Entrez
from Bio import Medline
MAX_COUNT = 10
TERM = 'Tuberculosis'
print('Getting {0} publications containing {1}...'.format(MAX_COUNT, TERM))
@arupgsh
arupgsh / example.com
Last active Feb 17, 2018
Nginx server configuration for running a CodeIgniter based site with PHP-FPM. https://www.wptron.com/configure-nginx-for-codeigniter/
View example.com
#Author: Arup Ghosh
#Description: https://gist.github.com/arupgsh/e50f4cd05547f0334412
#2016
server {
listen 80 default_server;
listen [::]:80 default_server ipv6only=on;
server_name example.com www.example.com;
root /var/www/example.com/public_html/;
index index.php;
View related-post-category.php
/** WPT related post widget */
function wpt_related_posts_cat() {
if ( is_single ( ) ) {
global $post;
$count = 1;
$postIDs = array( $post->ID );
$related = '';
$cats = wp_get_post_categories($post->ID );
$catIDs = array( );{
foreach ( $cats as $cat ) {
View pdbres.pl
print "Enter PDB File Name:";
$pdbn=<STDIN>;
print "Enter Output PDB File Name:";
$pdbo=<STDIN>;
print "Enter Chain Para 1:";
$pdbc1=<STDIN>;
print "Enter Chain Para 2:";
$pdbc2=<STDIN>;
print "Enter RES Para 1:";
$pdbr1=<STDIN>;
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