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@MartGro
MartGro / vectorbuilder link
Created March 3, 2025 14:26
Mammalian tissue specific promoter link
@MartGro
MartGro / rpy2_Deseq2_alternative_hypothesis.py
Created February 11, 2025 11:16
rpy2 DESeq2 Differential expression with alternative hypothesis
import rpy2.robjects as ro
from rpy2.robjects import pandas2ri, Formula
from rpy2.robjects.packages import importr
import pandas as pd
import numpy as np
from pathlib import Path
import matplotlib.pyplot as plt
# Enable conversion between pandas and R dataframes
pandas2ri.activate()
@MartGro
MartGro / pyDeseq2_snippet.py
Created February 11, 2025 10:16
pyDeseq2 Snippet that seems to work
import pydeseq2
from pydeseq2.dds import DeseqDataSet
from pydeseq2.ds import DeseqStats
import pandas as pd
import numpy as np
from itertools import combinations
from pathlib import Path
# Create output directory if it doesn't exist
import requests
import time
import logging
import json
from typing import Dict, List, Optional
from datetime import datetime
class EnsemblCompara:
def __init__(self, debug: bool = True):
self.base_url = "https://rest.ensembl.org"
import os
import re
from pathlib import Path
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from datetime import datetime
def parse_pdraw(pdraw_content):
https://bioconda.github.io/recipes/rmats/README.html
1) install it via conda
conda install rmats -c bioconda
2) check
which rmats.py
Places where you can find recordings of radio signals with different modulations:
https://www.sdrangel.org/iq-files/
https://www.sdrplay.com/iq-demo-files/
https://lucasteske.dev/satcom-projects/sample-baseband-files
@MartGro
MartGro / conda_dependencies.txt
Created August 30, 2023 12:16
Pangolin Conda Env
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
_libgcc_mutex=0.1=main
_openmp_mutex=5.1=1_gnu
argcomplete=3.1.1=pypi_0
argh=0.27.2=pypi_0
biopython=1.79=pypi_0
ca-certificates=2023.7.22=hbcca054_0
certifi=2016.9.26=py36_0
@MartGro
MartGro / RSP1_instructions.md
Last active February 12, 2023 08:44
Getting the RSP1 to run under Ubuntu 20.04
  1. Get the Driver

Download the driver from the following link:

https://www.sdrplay.com/dlfinishs/

  1. Follow the Instructions of CubicSDR

For instructions on how to build CubicSDR on Linux, refer to the following link:

@MartGro
MartGro / napari_image_display_widget.py
Created January 23, 2023 15:11
Simple Image Display Widget in Napari
import sys
from PyQt5.QtWidgets import QApplication, QLabel
from PyQt5.QtGui import QPixmap
class ImageWidget(QLabel):
"""
A QLabel widget that displays an image from a file
"""
def __init__(self, parent=None):
"""