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PoisonAlien / split_bdg_HM.sh
Created April 2, 2025 15:14
#!/bin/bash
#A minimal shell script to split the bedgraph with H/M info into H and M bedgraghs
if [ $# -ne 1 ]; then
echo "Usage: $0 <input_file.tsv>"
exit 1
fi
#input file and two H/M files
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PoisonAlien / PdfDeconstruct_fixed.tsx
Last active March 21, 2025 20:10
import React, { useEffect, useRef, useState } from 'react';
import * as d3 from 'd3';
import { Card, CardContent, CardDescription, CardHeader, CardTitle } from '@/components/ui/card';
import { ChevronRight, ChevronDown } from 'lucide-react';
interface NodeData {
name: string;
type?: string;
details?: string;
children?: NodeData[];
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PoisonAlien / json2D3.html
Created March 20, 2025 22:15
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Research Paper Visualization</title>
<script src="https://d3js.org/d3.v7.min.js"></script>
<style>
body {
font-family: Arial, sans-serif;
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PoisonAlien / icon_paths_full.tsv
Created February 22, 2025 12:47
category path
Machine_Learning https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/bsd/Machine_Learning/Facebook/PyTorch.svg
Machine_Learning https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/bsd/Machine_Learning/Google/Tensorflow.svg
Machine_Learning https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/bsd/Machine_Learning/Jupyter/Jupyter.svg
Amino-Acids https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Amino-Acids/B--Gideon-Bergheim/alanine_chem.svg
Amino-Acids https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Amino-Acids/B--Gideon-Bergheim/alanine_noH.svg
Amino-Acids https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Amino-Acids/B--Gideon-Bergheim/alanine.svg
Amino-Acids https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Amino-Acids/B--Gideon-Bergheim/amino_acid_back
@PoisonAlien
PoisonAlien / icon_path.tsv
Created February 18, 2025 21:28
We can make this file beautiful and searchable if this error is corrected: It looks like row 8 should actually have 2 columns, instead of 1 in line 7.
category path
Intracellular_components https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Intracellular_components/Simon_Dürr/zincfinger.svg
Intracellular_components https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Intracellular_components/ASE/histone_complex.svg
Intracellular_components https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Intracellular_components/ASE/histone_complex_acetylated.svg
Intracellular_components https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Intracellular_components/jaiganesh/mitochondria.svg
Intracellular_components https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Intracellular_components/jaiganesh/proteasome.svg
Intracellular_components https://raw.githubusercontent.com/duerrsimon/bioicons/refs/heads/main/static/icons/cc-0/Intracellular_components/jaiganesh/Endoplasmic_Reticulum.svg
Intracell
@PoisonAlien
PoisonAlien / timeline.mermaid
Last active October 13, 2024 16:57
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PoisonAlien / arcsum.Rmd
Last active August 28, 2024 05:34
---
title: "Sequencing run summary"
date: "Generated on: `r Sys.Date()`"
output:
html_document:
toc: true
toc_depth: 3
toc_float: true
self_contained: yes
theme: sandstone
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PoisonAlien / predict_gnomadAncestry.py
Last active July 17, 2024 17:17
#!/usr/bin/env python3
#A simple script to predict gnomAD ancestry using PCA loadings trained on gnomAD V3 datasets
#See here for details: https://gnomad.broadinstitute.org/news/2021-09-using-the-gnomad-ancestry-principal-components-analysis-loadings-and-random-forest-classifier-on-your-dataset/
#Author: Anand Mayakonda
import sys
import os.path
import shutil
import argparse
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PoisonAlien / bwview.sh
Created July 27, 2023 09:13
subset a bigWig file
#!/usr/bin/env bash
#Script to subset a bigWig file for user specific loci
#MIT License (Anand Mayakonda; [email protected])
function usage (){
echo "Subset a bigWig file for genomic loci.
Requires UCSC kentutils bigWigToBedGraph and bedGraphToBigWig to be installed
Binaries available from: https://hgdownload.soe.ucsc.edu/admin/exe/
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PoisonAlien / dl_vep_cache.sh
Created June 27, 2023 11:47
pipeline_dir = "./"
echo "Downloading VEP cache.." 1>&2
mkdir -p ${pipeline_dir}/resources/vep_cache/
cd ${pipeline_dir}/resources/vep_cache/
curl -O https://ftp.ensembl.org/pub/release-107/variation/indexed_vep_cache/homo_sapiens_vep_107_GRCh38.tar.gz
tar -xzf homo_sapiens_vep_107_GRCh38.tar.gz -C ./
wget https://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip -c Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz | bgzip > Homo_sapiens.GRCh38.dna.primary_assembly.fa.bgzip