🧣

Parashar parashardhapola

🧣

CEO @ NygenAnalytics | PhD in Computational biology. Working with single-cell genomics, scalable systems and cloud deployment

parashardhapola / umap_progress_bar.html

Created August 7, 2021 23:03

	<!DOCTYPE html>
	<html>
	<head><meta charset="utf-8" />
	<meta name="viewport" content="width=device-width, initial-scale=1.0">

	<title>umap_progress_bar</title><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js"></script><script>
	(function() {
	function addWidgetsRenderer() {
	var mimeElement = document.querySelector('script[type="application/vnd.jupyter.widget-view+json"]');
	var scriptElement = document.createElement('script');

parashardhapola / umap_progress_bar.ipynb

Created August 7, 2021 22:50

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parashardhapola / scRNA_Seq_fix_var.py

Created April 19, 2018 09:04

Remove mean variance trend in single cell RNA-Seq data

	import numpy as np
	import pandas as pd
	from statsmodels.nonparametric.smoothers_lowess import lowess

	def fix_var(gene_stats, n_bins = 200, lowess_frac = 0.4):

	# gene_stats is a dataframe with gene names as index (rownames) and two
	# columns:
	# 'm': mean value of each gene
	# 'v': variance of each gene

parashardhapola / quadFinder.py

Created August 10, 2016 12:27

Class for searching G-quadruplex motifs. (Part of QuadBase2 webserver)

	import re
	from itertools import groupby
	import os

	"""
	MIT License
	Copyright (c) [2016] [Parashar Dhapola]
	Permission is hereby granted, free of charge, to any person obtaining a copy
	of this software and associated documentation files (the "Software"), to deal
	in the Software without restriction, including without limitation the rights

parashardhapola / GeneImage.py

Last active May 10, 2024 15:23

A pure python code to draw gene diagrams with introns and exons and draw markers ('lollipops') at random positions on the gene

	import matplotlib.pyplot as plt

	"""
	MIT License
	Copyright (c) [2016] [Parashar Dhapola]
	Permission is hereby granted, free of charge, to any person obtaining a copy
	of this software and associated documentation files (the "Software"), to deal
	in the Software without restriction, including without limitation the rights
	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
	copies of the Software, and to permit persons to whom the Software is

parashardhapola / chrom_vis.py

Created July 18, 2016 06:19

A class for creating annotated chromosome maps (akin to ideograms sans bands) in pure python. Not fully tested but works for me.

	import numpy as np
	import matplotlib as mpl
	import matplotlib.pyplot as plt
	import pandas as pd # Not used here but will be required for creating dataframe
	import re
	import seaborn.apionly as sns

	"""
	MIT License

parashardhapola / cuffdiff_parser.py

Created July 17, 2016 10:36

	import sys
	import numpy as np

	class CuffDiff(object):
	def __init__(self, filename, up_log_fc_cutoff=1, down_log_fc_cutoff=-1, alpha=0.05):
	self.filename = filename
	self.upLogFCcutoff = up_log_fc_cutoff
	self.downLogFCcutoff = down_log_fc_cutoff
	self.alpha = alpha

parashardhapola / makeTSS.py

Created April 24, 2016 20:03

	import sys
	from warnings import warn
	import os

	__author__ = "Parashar Dhapola"
	__email__ = ""

	__desc__ = """
	This script converts whole gene coordinates into TSS coordinates.
	Ideally this script should work on any table downloaded form UCSC

parashardhapola / GTFparser.py

Created February 20, 2016 17:32

a small piece of code to easily hack into GTF files. Some features not optimized for large genomes so may hog on memory

	import sys
	from itertools import groupby

	def read_fasta(fasta_name):
	fh = open(fasta_name)
	faiter = (f[1] for f in groupby(fh, lambda line: line[0] == ">"))
	for head in faiter:
	head = head.next()[1:].strip()
	s = "".join(s.strip() for s in faiter.next())
	yield head, s

parashardhapola / flask_boilerplate_setup.bash

Created September 15, 2015 05:36

A small bash script to create skeleton of a FLASK based webserver and get running