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.
grabear
/ syntax.css
Created Nov 2, 2017
— forked from demisx/syntax.css
Syntax highlighter CSS file
View syntax.css
| .highlight { background: #ffffff; } | |
| .highlight .c { color: #999988; font-style: italic } /* Comment */ | |
| .highlight .err { color: #a61717; background-color: #e3d2d2 } /* Error */ | |
| .highlight .k { font-weight: bold } /* Keyword */ | |
| .highlight .o { font-weight: bold } /* Operator */ | |
| .highlight .cm { color: #999988; font-style: italic } /* Comment.Multiline */ | |
| .highlight .cp { color: #999999; font-weight: bold } /* Comment.Preproc */ | |
| .highlight .c1 { color: #999988; font-style: italic } /* Comment.Single */ | |
| .highlight .cs { color: #999999; font-weight: bold; font-style: italic } /* Comment.Special */ | |
| .highlight .gd { color: #000000; background-color: #ffdddd } /* Generic.Deleted */ |
grabear
/ SILVA_walkthrough.R
Last active Sep 18, 2020
Parsing .biom files with SILVA formatted annotations using phyloseq
View SILVA_walkthrough.R
| # 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") |
grabear
/ iSEE_plug.R
Created Aug 20, 2020
— forked from federicomarini/iSEE_plug.R
A function to wrap up the DESeq2 inputs&outputs, and plug that as SingleCellExperiment into iSEE
View iSEE_plug.R
| library(DESeq2) | |
| wrapup_for_iSEE <- function(dds, res) { | |
| # dds to vst | |
| vst <- vst(dds) | |
| # initialize the container | |
| se <- SummarizedExperiment( | |
| assays = List( | |
| counts = counts(dds), |
grabear
/ Newick2JSON.py
Created Apr 21, 2017
— forked from jhcepas/Newick2JSON.py
Converts a newick file into JSON format for d3/TreeWidget javascript component
View Newick2JSON.py
| import sys | |
| from ete2 import Tree | |
| import random | |
| def get_json(node): | |
| # Read ETE tag for duplication or speciation events | |
| if not hasattr(node, 'evoltype'): | |
| dup = random.sample(['N','Y'], 1)[0] | |
| elif node.evoltype == "S": | |
| dup = "N" |
grabear
/ Genomics_A_Programmers_Guide.md
Created Feb 18, 2020
— forked from andy-thomason/Genomics_A_Programmers_Guide.md
Genomics a programmers introduction
grabear
/ Genomics_A_Programmers_Guide.md
Created Feb 18, 2020
— forked from andy-thomason/Genomics_A_Programmers_Guide.md
Genomics a programmers introduction
View Genomics_A_Programmers_Guide.md
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.
View Adventuring_Gear.csv
| 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 |
grabear
/ pyenv-MCSR-build-log.txt
Created Mar 20, 2019
View pyenv-MCSR-build-log.txt
This file has been truncated, but you can view the full file.
| [r2294@sequoia ~ $] pyenv install -v 3.7.2 | |
| /tmp/python-build.20190320123301.27082 ~ | |
| /tmp/python-build.20190320123301.27082/Python-3.7.2 /tmp/python-build.20190320123301.27082 ~ | |
| Installing Python-3.7.2... | |
| checking build system type... x86_64-pc-linux-gnu | |
| checking host system type... x86_64-pc-linux-gnu | |
| checking for python3.7... python3.7 | |
| checking for --enable-universalsdk... no | |
| checking for --with-universal-archs... no |
grabear
/ Install demo for beRi Suite of Tools.md
Last active Oct 18, 2018
Install demo for beRi Suite of Tools
View Install demo for beRi Suite of Tools.md
beRi demo (tested on Ubuntu-16.04)
This demo was tested on Ubuntu-16.04 which comes pre-installed with bash, Python 3.6, git, and curl. The beRi package have been built using Python 3.6. Other versions of Python have not been tested. Other operating systems have not been tested. Know bugs include renv Issue #32
WARNING: USE THIS AT YOUR OWN RISK. THIS CODE IS UNTESTED.
beRi LICENSING: beRi
renv LICENSING: renv
grabear
/ docx_to_md.sh
Last active Apr 17, 2017
— forked from hugorodgerbrown/md_to_rst.sh
Shell script for converting a batch of *.md files into *.rst using pandoc.
View docx_to_md.sh
| # This script was created to convert a directory full | |
| # of Word Document (.docx) files into .md equivalents. It uses | |
| # pandoc to do the conversion. | |
| # | |
| # 1. Install pandoc from http://johnmacfarlane.net/pandoc/ | |
| # 2. Copy this script into the directory containing the .md files | |
| # 3. Ensure that the script has execute permissions | |
| # 4. Run the script | |
| # By default this will keep the original .md file |