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R. Eric Collins rec3141

  • University of Alaska Fairbanks
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View d3.phylogram.js
/*
d3.phylogram.js
Wrapper around a d3-based phylogram (tree where branch lengths are scaled)
Also includes a radial dendrogram visualization (branch lengths not scaled)
along with some helper methods for building angled-branch trees.
d3.phylogram.build(selector, nodes, options)
Creates a phylogram.
Arguments:
selector: selector of an element that will contain the SVG
View d3.phylogram.js
/*
d3.phylogram.js
Wrapper around a d3-based phylogram (tree where branch lengths are scaled)
Also includes a radial dendrogram visualization (branch lengths not scaled)
along with some helper methods for building angled-branch trees.
d3.phylogram.build(selector, nodes, options)
Creates a phylogram.
Arguments:
selector: selector of an element that will contain the SVG
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rec3141 / lsa_mds.R
Created December 11, 2013 23:50 — forked from meefen/lsa_mds.R
View lsa_mds.R
# load required libraries
library(tm)
library(ggplot2)
library(lsa)
# 1. Prepare mock data
text <- c("transporting food by cars will cause global warming. so we should go local.",
"we should try to convince our parents to stop using cars because it will cause global warming.",
"some food, such as mongo, requires a warm weather to grow. so they have to be transported to canada.",
"a typical electronic circuit can be built with a battery, a bulb, and a switch.",
@rec3141
rec3141 / gist:b2cc9d192d214687b575ab0cce02f5f8
Created February 9, 2018 07:18
bash reference manager: get DOI from titles
View gist:b2cc9d192d214687b575ab0cce02f5f8
while read line; do title=`echo $line | sed 's/ /+/g'`; curl -s https://api.crossref.org/works?query.title=$title&rows=1 | tr ',' '\n' | tr -d '"\' | grep ^DOI | cut -f2- -d':'; done < titles.txt > titles.bib
@rec3141
rec3141 / gist:c6f318ae79e9695af6af14d04963f554
Created February 9, 2018 07:21
bash reference manager: get bibtext from DOIs
View gist:c6f318ae79e9695af6af14d04963f554
while read line; do curl -LH "Accept: application/x-bibtex" https://doi.org/$line | grep -v '^\s*[<"]'; done < dois.txt > dois.bib
@rec3141
rec3141 / gist:24090e42b4487635e8ac9f5c566ff417
Created February 9, 2018 10:28
get a bibtext file from a text reference list
View gist:24090e42b4487635e8ac9f5c566ff417
while read line; do curl -s "https ://api.crossref.org/works?query=`echo $line | tr -sC '[^a-zA-Z]' '+'`" | tr "," "\n" | tr -d '"\' | grep ^DOI | cut -f2- -d':' | head -n1 | xargs -I{} curl -sLH "Accept: application/x-bibtex" https ://doi.org/{} | grep -v '^\s*[<"]'; done < file
@rec3141
rec3141 / run-hmmer.sh
Created April 6, 2018 00:45
run-hmmer.sh
View run-hmmer.sh
#!/bin/sh
# run hmmer using hmm files
#INDIR=$1 #directory to search for .fastq.gz files
INDIR=~/work/NPRB
cd ~/work/hmm
for hmmfile in *.hmm; do
hmm=`basename $hmmfile .hmm`;
@rec3141
rec3141 / srun-metaspades.sh
Created April 6, 2018 01:26
srun-metaspades.sh
View srun-metaspades.sh
#!/bin/bash
NODE=bio
THREADS=7 #7 for bio, 24 for t1small
MEM=200 #128 max for t1small, 200+ for bio
mkdir -p spades-assembly
DIR='.'
#NPRB_meta_TBS.04.MEIO.R1.trimmed.fastq.gz
for PREFIX in `ls *.trimmed.fastq.gz | cut -f1-3 -d'.' | sort -u `; do
View gist:4c2cadec8e62683636d32ab52146bd7f
head -n1000 18*R1.fastq | grep -v -e '==> 18' -e '^$' | paste - - - - | cut -f2 | sort | uniq -c | sort -rn | head -n1000 | catg > 18s-top1000f.fa