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.
Rob Gilmore grabear
👨🔬
grabear
/ iSEE_plug.R
Created
August 20, 2020 17:18
— forked from federicomarini/iSEE_plug.R
A function to wrap up the DESeq2 inputs&outputs, and plug that as SingleCellExperiment into iSEE
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ Genomics_A_Programmers_Guide.md
Created
February 18, 2020 14:36
— forked from andy-thomason/Genomics_A_Programmers_Guide.md
Genomics a programmers introduction
grabear
/ Genomics_A_Programmers_Guide.md
Created
February 18, 2020 14:36
— forked from andy-thomason/Genomics_A_Programmers_Guide.md
Genomics a programmers introduction
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.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
March 20, 2019 17:38
This file has been truncated, but you can view the full file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [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 | |
| checking MACHDEP... checking for --without-gcc... no |
grabear
/ Install demo for beRi Suite of Tools.md
Last active
October 18, 2018 22:59
Install demo for beRi Suite of Tools
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
/ SILVA_walkthrough.R
Last active
September 18, 2020 13:01
Parsing .biom files with SILVA formatted annotations using phyloseq
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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
/ syntax.css
Created
November 2, 2017 20:26
— forked from demisx/syntax.css
Syntax highlighter CSS file
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| .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
/ Newick2JSON.py
Created
April 21, 2017 19:21
— forked from jhcepas/Newick2JSON.py
Converts a newick file into JSON format for d3/TreeWidget javascript component
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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
/ docx_to_md.sh
Last active
April 17, 2017 01:16
— forked from hugorodgerbrown/md_to_rst.sh
Shell script for converting a batch of *.md files into *.rst using pandoc.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |