Bernie Pope

Login: bjpop

Company: null

Location: null

Bio: null

Blog: http://www.berniepope.id.au/

Blog: http://www.berniepope.id.au/

Repositories

acm_icpc

Solutions to ACM ICPC programming competition questions

annokey

Annotation of gene lists with keyword hits from the NCBI gene database

anonymise

A program to edit fields in a bam file

asteroids

A clone of the asteroids game using the Pygame library

bamcover

Plot graphs of read coverage for BAM files

bam_gene_coverage

null

banzai

null

berp

An implementation of Python 3

bionitio-csharp

Demonstrating best practices for bioinformatics command line tools

biotool

Proverbial biotool implemented in multiple languages

blip

A bytecode compiler for Python 3

chop_fasta

Chop FASTA files up into separate sequences, output one per file

cnv_analysis

CNV analysis tools

cnvcanon

Canonify CNV calls

coauthorgraph

Plot graph of coauthorship given a bibtex file

coglabweb

Website for the Colorectal Oncogenomics Group

collapse_cnvs

null

complexo_pipeline

A pipeline for calling variants

cosmology_example

An example cosmology program

crpipe

Bioinformatics pipeline based on Ruffus

cwl_explorer

Interactive visualisation of CWL workflows

dump_eic

null

fampipeline

null

favr

Filtering and Annotation of Variants that are Rare

favr-indel

FAVR indel

fcctx_caller_agreement

Agreement between CNV callers

fcctx_replicate_agreement

null

file_usage

Summary of file usage in a top down manner

haskell-linux-perf

Haskell library for reading perf.data files from the linux performance events tool.

haskell-mpi

MPI bindings for Haskell

haskell-sprng

Haskell binding to the SPRNG library

hiplex-website

Website for Hi-Plex

HiTIME

High-resolution Twin-Ion Metabolic Extraction

HiTIME-CPP

null

hts-specs

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

insighter

null

jobscript_generator

An interactive webpage for generating job scripts for the SLURM scheduler

js-turtle

Turtle graphics in Javascript using HTML5 canvas

language-python

A parser for Python 2.x and 3.x written in Haskell

language-python-test

Code for testing the language-python library

lbc_var_annotate_sens_spec

null

lfg

A lagged fibonacci generator in Haskell

lynch_gatk

GATK variant calling pipeline for Suspected Lynch Syndrome project

make-pbs-script

Automate the creation of simple PBS scripts, using a question and answer dialog

md5_pipeline

A pipeline for running md5 checksums over many files in parallel

methpat

A program for summarising CpG methylation patterns

methyl_bismark_methpat

A pipeline for running bismark and methpat on methylation data

ministg

Ministg is an interpreter for a high-level, small-step, operational semantics for the STG machine.

mpi-article-monad-reader

Article about the Haskell MPI bindings for the Monad.Reader magazine

ngs-pipeline

Next generation sequencing pipeline

offtarget

Plot offtarget reads for targeted sequence data

ovarian_cancer_pipeline

Somatic variant calling pipeline for ovarian cancer

pbs2slurm

Tool for converting PBS/Torque scripts into SLURM scripts

pipeline_base

Infrastructure for bioinformatics pipelines based on Ruffus

pipeline_yaml

null

plot_enrolments

Plot a graph of student enrolments using downloaded CSV file from LMS

pyray

Ray tracer in Python

python_cheat_sheet_notebook

Python cheat sheet notebook

python_physics_sample_solutions

null

python_rainfall_ipython

IPython example using rainfall data

raft_hotspots_se

Compute DNA double stranded breakpoint hotspots from RAFT sequencing data

rover

Read overlap variant caller.

rubra

Infrastructure code to support DNA pipeline

ruffus

Ruffus is a lightweight python module for running computational pipelines.

saveSvgAsPng

null

scala-fungraph

Functional graphics in Scala

skynet

test csharp bionitio

snp_similarity

Compare all-to-all samples for SNP similarity

srst2

Short Read Sequence Typing for Bacterial Pathogens

stackage

"Stable Hackage": vetted consistent packages from Hackage

stacker

null

svdistil

null

svfilter

Filter for structural variants

SWinC

null

test_ruffus_pipeline

A simple Ruffus pipeline for testing purposes

twin_ion_pipeline

A pipeline for detecting twin ion signals in LCMS data

undr_rover

Unmapped primer directed ROVER

vimrc

My vimrc file

website

My website

Commits To