Kaan Ihsan Eskut eskutkaan

Doctoral candidate. Bioinformatics and Computational Biology.

eskutkaan / median_of_ratios_normalization_v1.r

Created October 7, 2024 19:27

	library(dplyr)
	library(tibble)
	data = read.csv("gene_count_matrix.csv", row.names = "gene_id")
	head(data)
	log_data = log(data)
	head(log_data)


	log_data = log_data %>%
	rownames_to_column('gene') %>%

eskutkaan / wip_suffix_search.c

Created July 8, 2024 16:16

wip_suffix_search

	#include <stdio.h>
	#include <stdlib.h>
	#include <string.h>

	// Function to compare suffixes for qsort
	int suffix_compare(const void a, const void b) {
	return strcmp((const char )a, (const char **)b);
	}

	// Function to construct the suffix array

eskutkaan / filter_fasta_by_list_of_headers.py

Created November 8, 2023 18:54

	#!/usr/bin/env python3


	# Usage
	# python3 filter_fasta_by_list_of_headers.py [fasta.file] [header.list] > [output.file]


	from Bio import SeqIO
	import sys

eskutkaan / check_gtf_entries.py

Created November 8, 2023 18:49

	#!/usr/bin/env python3

	import argparse
	import csv
	import natsort
	import pandas

	# Parse arguments
	parser = argparse.ArgumentParser()
	parser.add_argument(

eskutkaan / gtf_merge_name_and_id.py

Created November 8, 2023 18:43

	# Define a function to extract the value of a specified attribute
	def extract_attribute_value(line, attribute):
	start = line.find(attribute) + len(attribute) + 2 # +2 to skip the attribute name and the initial space
	end = line.find('";', start)
	return line[start:end]

	# Read the input file
	input_filename = "trial.gtf"
	output_filename = "output_trial.gtf"