klmr

thesis

My PhD thesis, “Investigating the link between tRNA and mRNA abundance in mammals”

lisp.cpp

Minimal Lisp implementation in C++, inspired by “lispy”

trna

tRNA gene regulation downstream analysis

cv

Resume

system-setup

Bootstrap a usable system configuration for OS X

te

Map, quantify and analyse transposable element expression

vim-snakemake

Snakemake Vim definitions, copied from https://bitbucket.org/snakemake/snakemake/

codons

Analysis of adaptation of translation efficiency by means of codon–anticodon selection

ggraph

Grammar of Graph Graphics

pichip

poly-u

rnaseq-norm

Presentation slides about RNA-seq normalisation methods

roxydoxy

sciencefair

The open source p2p desktop science library that puts users in control :microscope: :book:

shiny

Easy interactive web applications with R

altrepisode

Example altrep and C++ R :package:

BiocWorkflow2016

Files for a Bioconductor workflow for low-level scRNA-seq data analyses.

gzip-huffman-tree

Prints the Huffman table for a gzip file

homebrew-dupes

System duplicate formulae for the Homebrew package manager

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

igv.js-jupyter

Extension for Jupyter Notebook which integrates igv.js

maketools

Tools for GNU make

mcm5s2U

Analysis of data from Alper’s mcm5s2U project

minted

minted is a package that facilitates expressive syntax highlighting in LaTeX using the powerful Pygments library. The package also provides options to customize the highlighted source code output using fancyvrb.

modeest

Mode estimation in R

pol3-seq

Genome-wide repeat coverage analysis of pol III ChIP

queuosine

R-Vim-runtime

Vim runtime scripts of file types that include R code

srna-seq-course

Scripts for a smallRNA-seq analysis course

stressed-mice