taoliu

#!/bin/bash
#
# This script will find the consensus peak regions from peak files (in
# BED format) of multiple samples by:
#
# 1. Converting the peak file of each sample into non-overlapping 3
# cols BED file and concatenating them;
#
# 2. Sorting the concatenated file and Building a genome coverage
# track in BedGraph, of which the value (the 3rd col) indicates the

taoliu

# K-nearest neighbor smoothing based on sNN from clustering
# Inspired by knn-smooth.R: https://github.com/yanailab/knn-smoothing/blob/master/knn_smooth.R
# by Tao Liu <vladimir.liu@gmail.com>

#' kNN-smoothing on a given matrix based on a pre-calculated sNN matrix
#'
#' Note: sparse matrix will be converted to regular matrix, so memory
#' usage will be high.
#'
#' @param M A numeric matrix that will be smoothed. It should have

taoliu

#!/usr/bin/env python

# This script is a wrapper in Python to help submit jobs, that need to use CONDA environment, to SLURM.

import subprocess
import sys
import os
import time
import argparse as ap