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Rob Gilmore grabear

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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),
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.

https://www.genomicsplc.com

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.

https://www.genomicsplc.com

@grabear
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
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
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
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