Skip to content

Instantly share code, notes, and snippets.

View jrherr's full-sized avatar
💭
Probably working

Josh Herr jrherr

💭
Probably working
152 followers · 135 following
View GitHub Profile
@jrherr
jrherr / excel_my_barplot.R
Created January 13, 2016 16:07 — forked from mw55309/excel_my_barplot.R
R code to create Excel-like barplot
x <- data.frame(d=runif(12), g=rep(1:4, each =3))
my.col <- c("deepskyblue3","darkorange2","darkgray","gold")
spacer <- c(1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1)
bw <- 0.8
xmax <- (sum(spacer) * bw) + (nrow(x) * bw)
@jrherr
jrherr / read_hdf5_biom.R
Created December 8, 2015 17:55 — forked from jnpaulson/read_hdf5_biom.R
Hacks to load an hdf5 biom file and be able to add it to metagenomeSeq or phyloseq
source("http://bioconductor.org/biocLite.R")
biocLite(c("rhdf5","biom"))
library(rhdf5)
library(biom)
# This generates the matrix columns-wise
generate_matrix <- function(x){
indptr = x$sample$matrix$indptr+1
indices = x$sample$matrix$indices+1
data = x$sample$matrix$data
@jrherr
jrherr / fq-strip-contam.sh
Last active September 9, 2015 15:28 — forked from standage/fq-strip-contam.sh
Procedure for removing contaminants from paired-end sequence data. The bwa-mem algorithm is used to map reads against a database of contaminants, a small Perl one-liner is used to filter out reads that map to the contaminants, the SAM data is converted to BAM format, which is then fed (via process substitution) to Tophat's bam2fastx to convert b…
# -q: output in Fastq format
# -Q: ignore BAM quality flags
# -P: paired-end data
bam2fastx -qQP -o clean.fq <(bwa mem contaminants.fasta reads.1.fq reads.2.fq | \
perl -ne '@v = split(/\t/); print if(m/^@/ or ($v[1] & 4 and $v[1] & 8))' | \
samtools view -bhS -)
@jrherr
jrherr / genome_plots.r
Last active August 29, 2015 14:27 — forked from roblanf/genome_plots.r
Make plots about genome sequencing, size, and gene content
source("http://bioconductor.org/biocLite.R")
biocLite("genomes")
library(genomes)
library(ggplot2)
valid <- c("released", "created", "submitted")
data(proks)
update(proks)
@jrherr
jrherr / search_download.md
Last active August 29, 2015 14:26 — forked from sckott/search_download.md
occ_search and occ_download

to get similar results for GBIF search and download APIs

Load rgbif

library("rgbif")

occ_search() method

@jrherr
jrherr / 01.cmake
Last active August 29, 2015 14:22 — forked from anonymous/01.cmake
Wed Jun 10 19:52:40 +0000 2015
cmake
..
-DCMAKE_C_FLAGS_RELEASE=
-DCMAKE_CXX_FLAGS_RELEASE=
-DCMAKE_INSTALL_PREFIX=/home/ubuntu/.linuxbrew/Cellar/spades/3.5.0
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_FIND_FRAMEWORK=LAST
-DCMAKE_VERBOSE_MAKEFILE=ON
@jrherr
jrherr / bamfilter_oneliners.md
Last active September 9, 2015 15:19 — forked from davfre/bamfilter_oneliners.md
@jrherr
jrherr / missing.R
Created August 23, 2014 18:33 — forked from vsbuffalo/missing.R
# A quick function to save a PBM (http://en.wikipedia.org/wiki/Netpbm_format)
# visualize *a lot* of missing data pretty quickly (outside of R).
writeMissingPBM <- function(x, file) {
dims <- dim(x)
x[] <- as.integer(is.na(x))
con <- file(file, open="wt")
writeLines(sprintf("P1\n%d %d", ncol(x), nrow(x)), con)
write.table(x, file=con, sep=" ", col.names=FALSE, row.names=FALSE, quote=FALSE)
close(con)
@jrherr
jrherr / gist:8910228
Created February 10, 2014 04:09 — forked from pithyless/gist:1208841

Install Python

$ brew install readline sqlite gdbm
$ brew install python --universal --framework
$ python --version
Python 2.7

Symlinks...

@jrherr
jrherr / zany.R
Created December 18, 2013 02:18 — forked from johnmyleswhite/zany.R
M <- matrix(c(1, 0, 0, 1), byrow = 1, nrow = 2)
df <- data.frame(A = 1)
df$B <- list(M)
df
# A B
# 1 1, 0, 0, 1