Anand Mayakonda PoisonAlien
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| #!/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/ |
PoisonAlien
/ predict_gnomadAncestry.py
Last active
July 17, 2024 17:17
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| #!/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 |
PoisonAlien
/ arcsum.Rmd
Last active
August 28, 2024 05:34
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| --- | |
| 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 |
PoisonAlien
/ timeline.mermaid
Last active
October 13, 2024 16:57
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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.
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| 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
/ icon_paths_full.tsv
Created
February 22, 2025 12:47
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| 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
/ json2D3.html
Created
March 20, 2025 22:15
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| <!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; |
PoisonAlien
/ PdfDeconstruct_fixed.tsx
Last active
March 21, 2025 20:10
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| 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[]; |
PoisonAlien
/ split_bdg_HM.sh
Created
April 2, 2025 15:14
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| #!/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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