afrendeiro

import numpy as np
import matplotlib.pyplot as plt


# class from here: http://nbviewer.ipython.org/gist/tillahoffmann/f844bce2ec264c1c8cb5
class gaussian_kde(object):
    """Representation of a kernel-density estimate using Gaussian kernels.

    Kernel density estimation is a way to estimate the probability density
    function (PDF) of a random variable in a non-parametric way.

afrendeiro

#!/bin/sh

# Flacon-style convert to mp3 and split tracks from flac+cue files
# Made by André Rendeiro (afrendeiro@gmail.com)

# Rename
{
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done

afrendeiro

Introduction to linux command line/ipython/git/R for bioinformatics:

• https://github.com/biom262/biom262-2016
• https://github.com/ricket-sjtu/bi028
• https://github.com/YeoLab/single-cell-bioinformatics/
• https://github.com/YeoLab/single-cell-bioinformatics/tree/master/notebooks
• https://github.com/ltminty/Bioinformatics-and-R/blob/master/Rbioinformatics.ipynb

RNA-seq:

• https://github.com/Caroldm/RNA-Seq-Tutorial---Jupyter-notebook/blob/master/RNAseq%20tutorial.ipynb

afrendeiro

#!/usr/bin/env uv --script

# /// script
# dependencies = [
#   "numpy",
#   "squidpy>=1.6.5",
#   "scikit-network",
# ]
# python_version = ">=3.12"
# ///

afrendeiro

#!/bin/bash

set -e

INPUT="$1"
EXT="${INPUT##*.}"
BASENAME=$(basename "$INPUT" ."$EXT")
INPUT_DIR=$(dirname "$(realpath "$INPUT")")
TMPDIR=$(mktemp -d)

afrendeiro

#!/usr/bin/env python

"""
Get a GEO series matrix file describing an experiment and
parse it into project level and sample level data.
"""

import os
from typing import Tuple, Union
import tempfile

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# /// script
# dependencies = [
#   "numpy",
#   "pandas",
#   "statsmodels",
#   "scikit-learn",
#   "scikit-bio",
#   "matplotlib",
# ]
# ///

afrendeiro

# New users
sudo adduser username

# Grant the new user sudo privileges
sudo visudo
# username ALL=(ALL:ALL) ALL
# add this line ^^

# change to that user
su - username

afrendeiro

afrendeiro

#! python3.7

import argparse
import os
import numpy as np
import speech_recognition as sr
import whisper
import torch

from datetime import datetime, timedelta