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
/ 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
/ 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.
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
/ 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
/ 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 |