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@grabear
grabear / Adventuring_Gear.csv
Last active June 26, 2019 18:27
LST file parser
Equipment_Name RANGE TYPE OUTPUTNAME WT CRITMULT Equipment_Name CONTAINS COST PROFICIENCY SORTKEY CRITRANGE DESC SPROP DAMAGE SIZE KEY SOURCEPAGE QUALITY
Backpack Goods.Container.General.Resizable 2 Backpack UNLIM|Any 2 Backpack Backpack p.158
Barrel Goods.Container.General 30 Barrel UNLIM|Any 2 Barrel Barrel p.158
Basket Goods.Container.General 1 Basket UNLIM|Any 0.4 Basket Basket p.158
Bedroll Goods.General.Resizable 5 Bedroll 0.1 Bedroll Bedroll p.158
Bell Goods.General 0 Bell 1 Bell Bell p.158
Blanket, Winter Goods.General.Resizable Winter Blanket 3 Blanket, Winter 0.5 Blanket, Winter Blanket (Winter) p.158
Block and Tackle Goods.General 5 Block and Tackle 5 Block and Tackle Block and Tackle p.158
Bottle Goods.Container.General 1 Bottle 1.5|Liquid=3 2 Bottle Bottle (Glass) p.158
Bucket Goods.Container.General 2 Bucket UNLIM|Any 0.5 Bucket Bucket p.158
@andy-thomason
andy-thomason / Genomics_A_Programmers_Guide.md
Created May 14, 2019 13:32
Genomics a programmers introduction

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

@federicomarini
federicomarini / iSEE_plug.R
Last active April 20, 2023 09:54
A function to wrap up the DESeq2 inputs&outputs, and plug that as SingleCellExperiment into iSEE
library(DESeq2)
wrapup_for_iSEE <- function(dds, res) {
# dds to vst
vst <- vst(dds)
# initialize the container
se <- SummarizedExperiment(
assays = List(
counts = counts(dds),
@Liam0205
Liam0205 / install_vim.sh
Created November 2, 2018 03:17
Compile and install VIM on CentOS 6.x without root.
#!/bin/bash
git clone https://github.com/vim/vim.git --depth=1
cd vim
make -p $HOME/local/bin
./configure --prefix=$HOME/local/vim --enable-multibyte --with-tlib=tinfo --enable-pythoninterp --enable-rubyinterp --with-ruby-command=/usr/bin/ruby --with-features=huge
make -j24
make install
cd $HOME/local/bin
for file in $(ls $HOME/local/vim/bin); do ln -sf $HOME/local/vim/bin/$file $file; done
@grabear
grabear / SILVA_walkthrough.R
Last active September 18, 2020 13:01
Parsing .biom files with SILVA formatted annotations using phyloseq
# This functionality has been tested and a PR has been pulled with phyloseq here:
# https://github.com/joey711/phyloseq/pull/854
#
# While the function has been vetted, the maintainers are very busy and the PR has not
# yet been added to the main package. Below i've added some detail to explain how to parse
# your silva data. It's quite easy....
source("parse_silva_taxonomy_128")
@sdhutchins
sdhutchins / mygene_example.py
Last active January 26, 2017 19:34
MyGeneExample - Gene list to DataFrame to CSV file
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 13 18:18:52 2017
@author: sdhutchins
"""
#------------------------------------------------------------------------------
# Modules Used
#------------------------------------------------------------------------------
@dschep
dschep / raspbian-python3.6.rst
Last active October 24, 2023 14:57 — forked from BMeu/raspbian-python3.5.rst
Installing Python 3.6 on Raspbian

Installing Python 3.6 on Raspbian

As of January 2018, Raspbian does not yet include the latest Python release, Python 3.6. This means we will have to build it ourselves, and here is how to do it. There is also an ansible role attached that automates it all for you.

  1. Install the required build-tools (some might already be installed on your system).

    2. 




  


  




    


          
    

      

        
        

          

              @0xjac
          

          

            
                0xjac
                / private_fork.md
            
            

              Last active
              May 3, 2024 18:34
            

              
                Create a private fork of a public repository
              
          

        

      

        

  

      

    
The repository for the assignment is public and Github does not allow the creation of private forks for public repositories.


The correct way of creating a private frok by duplicating the repo is documented here.


For this assignment the commands are:


    

  1. Create a bare clone of the repository.
(This is temporary and will be removed so just do it wherever.)

    

    2. 



git clone --bare git@github.com:usi-systems/easytrace.git



  


  




    


          
    

      

        
        

          

              @walterst
          

          

            
                walterst
                / create_majority_taxonomy.py
            
            

              Created
              July 8, 2015 18:43
            

              
                See help text below about usage. Script was created to create 90% majority taxonomy strings for all sequence taxa strings in the Silva 119 release.
              
          

        

      

        

  

    
    


        



  


  

        

          
          #!/usr/bin/env python
        

        

          
          

        

        

          
          # USAGE
        

        

          
          # python create_majority_taxonomy.py X Y Z A
        

        

          
          # where X is the taxonomy mapping file for all NR seqs, Y is the representative
        

        

          
          # file (i.e. one of the rep_set/ files with the 119 release), Z is the OTU 
        

        

          
          # mapping file created from running pick_otus.py, and A is the output 
        

        

          
          # consensus mapping file
        

        

          
          

        

        

          
          from sys import argv
        

  





    


  




    


          
    

      

        
        

          

              @walterst
          

          

            
                walterst
                / create_consensus_taxonomy.py
            
            

              Created
              July 8, 2015 18:41
            

              
                See help text below about usage. Script was created to create consensus taxonomy strings for all sequence taxa strings in the Silva 119 release.
              
          

        

      

        

  

    
    


        



  


  

        

          
          #!/usr/bin/env python
        

        

          
          

        

        

          
          # USAGE
        

        

          
          # python create_consensus_taxonomy.py X Y Z A
        

        

          
          # where X is the taxonomy mapping file for all NR seqs, Y is the representative
        

        

          
          # file (i.e. one of the rep_set/ files with the 119 release), Z is the OTU 
        

        

          
          # mapping file created from running pick_otus.py, and A is the output 
        

        

          
          # consensus mapping file
        

        

          
          

        

        

          
          from sys import argv