ckandoth

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

Instead of the official instructions, we will use conda to install VEP and its dependencies. If you don't already have conda, install it into $HOME/miniconda3 as follows:

curl -sL https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh -o /tmp/miniconda.sh
sh /tmp/miniconda.sh -bfp $HOME/miniconda3

Add the conda bin folder into your $PATH so that all installed tools are accessible via command-line. You can also add this to your ~/.bashrc

kovetskiy

#!/bin/bash
###
### my-script — does one thing well
###
### Usage:
###   my-script <input> <output>
###
### Options:
###   <input>   Input file to read.
###   <output>  Output file to write. Use '-' for stdout.

pgm

import argparse
import sqlite3
import sys
import numpy as np
import pandas as pd


def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("in_csv_0")

mutterer

// this example uses the Toolbar.setIcon(toolName,icon) method
// added in v1.53h, to dynamically update its icon.

macro "Left Eye Action Tool - N44 C000 o00nn" {
  setTool("Googly Eyes Tool")
}
macro "Right Eye Action Tool - N44 C000 o00nn" {
  setTool("Googly Eyes Tool")
}

aileftech

$ grep -P "^[ABCDEFabcdefOoIi]{6,6}$" /usr/share/dict/words | tr 'OoIi' '0011' | tr '[:lower:]' '[:upper:]' | awk '{print "#" $0}' 
#ACAD1A
#B0BB1E
#DEBB1E
#AB1DED
#ACAC1A
#ACCEDE
#AC1D1C
#BAB1ED
#BA0BAB

veekaybee

Anti-hype LLM reading list

Goals: Add links that are reasonable and good explanations of how stuff works. No hype and no vendor content if possible. Practical first-hand accounts of models in prod eagerly sought.

Foundational Concepts

Pre-Transformer Models