Wolfgang Resch - Notes

2014
Nov 18 — Process a VCF file with htslib
Jul 19 — How to model dwell time of proteins on DNA binding sites in R - part 1
Jun 27 — Visualizing algorithms - an article by Mike Bostock
Jun 26 — Smoothing data with Savitzky-Golay filters
Jun 26 — Use newline or tab in replacement with `replace-string` or `replace-regexp` in emacs
May 22 — Aligning ggplot2 graphs on a page
May 7 — Bash named pipes and process substitution
May 6 — Matching up homologous genes from different organisms with homologene
Apr 24 — Short circuit evaluation of conditionals in bash
Apr 8 — Make tutorial slides geared towards bioinformatics pipelines
Mar 27 — Parallel execution of R code with the multicore package
Mar 26 — PBS job arrays
Feb 28 — Bash module mailcmd
Feb 27 — Background processes, nohup, and disowning your children
Feb 19 — Insert size distribution from paired-end bam files
Jan 31 — Merging bigwig files
2013
Jul 24 — Running a command with a timeout
Jul 11 — How to pick a random subset of lines from file
Jun 24 — Picking illumina index sequence combinations
Jun 21 — Automatically fetch PDFs of UCSC browser views for locations within a given session
Jun 20 — Passing command line arguments into R scripts
Jun 13 — A fun (if hacky) way to determine fastq score types in bash
Jun 12 — Safe locking mechanism in bash to serialize access to some resource
Mar 8 — Inverse hyperbolic sine transformation for ggplot2 using scales
Jan 28 — R project template
Jan 11 — figshare - sharing (unlimited) information publicly with a doi
2012
Dec 12 — .bash_profile vs. .bashrc
Dec 10 — Splitting bash pipelines
Dec 6 — CDE - a tool for reproducible research and application packaging using application virtualization
Nov 30 — Modify splom to use hexbin panels and show pearson correlations
Nov 28 — Faster tunneling of X11 over ssh
Nov 7 — Target specific variables in makefiles
Nov 6 — Create smoothscatter like plots with ggplot2
Nov 2 — Subplots with ggplot2
Nov 1 — Qsub submit jobs from makefile
Oct 31 — Run commands on remote machine with ssh
Oct 31 — Preserve intermediate targets in chains of implicit rules in makefiles
Oct 25 — Use xargs to execute jobs in parallel
2010
Jun 10 — Python pipelines with generators and coroutines