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# /// script | |
# dependencies = [ | |
# "numpy", | |
# "pandas", | |
# "statsmodels", | |
# "scikit-learn", | |
# "scikit-bio", | |
# "matplotlib", | |
# ] | |
# /// |
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# 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 |
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#!/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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#!/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 |
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#! python3.7 | |
import argparse | |
import os | |
import numpy as np | |
import speech_recognition as sr | |
import whisper | |
import torch | |
from datetime import datetime, timedelta |
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#!/bin/bash | |
# Terminate on first error | |
set -e | |
# Check if input file is provided | |
if [ -z "$1" ]; then | |
echo "Usage: $0 <input_file.pdf>" | |
exit 1 | |
fi |
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""" | |
Re-analyze GeoMx data from Rendeiro et al. 2021 doi:s41586-021-03475-6 | |
Requirements (Python 3.10+): | |
pip install \ | |
"anndata" \ | |
"matplotlib>=3.8.3" \ | |
"numpy>=1.26.4" \ | |
"pandas>=2.1.0" \ | |
"scanpy" \ |
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from pathlib import Path | |
import parmap | |
import requests | |
def update(gsll): | |
return [g for g in gsll if not (output_dir / (g + ".gmt")).exists()] | |
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