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  • Garvan Institute of Medical Research
  • Sydney, Australia

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A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.

10,483 632 Updated Apr 3, 2025

Useful bash one-liners for bioinformatics.

1,928 521 Updated Sep 9, 2023

Polygenic score calculation from VCF in Nim.

Nim 15 3 Updated Nov 22, 2020

hybrid assembly pipeline for bacterial genomes

C++ 601 138 Updated Jul 25, 2024

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

Jupyter Notebook 137 40 Updated Jun 2, 2021

A (mostly) universal methylation extractor for BS-seq experiments.

C 172 45 Updated Jun 21, 2024

A Rmarkdown editor with instant preview

R 345 28 Updated Oct 27, 2016

See:

C# 18 1 Updated Jan 19, 2015

create, manage, and upload track hubs for use in the UCSC genome browser

Python 54 20 Updated Apr 20, 2024

significance testing over interval overlaps

Python 30 10 Updated Jul 11, 2020

a package to handle ChromHMM (http://compbio.mit.edu/ChromHMM/) and similar segmentation models in R

R 8 3 Updated Oct 4, 2024

R imgur API Client

R 16 3 Updated Apr 22, 2018

CGAT-ruffus is a lightweight python module for running computational pipelines

Python 174 34 Updated Jul 12, 2021

Resumes generated using the GitHub informations

JavaScript 62,520 1,356 Updated Feb 15, 2023

Multiscale representation of genomic signals

MATLAB 13 7 Updated Jan 31, 2017

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

Python 149 57 Updated Aug 22, 2024

methylation sequence data quality assessment tool

C 6 1 Updated Aug 17, 2018

A program for summarising CpG methylation patterns

Python 20 5 Updated Sep 9, 2016

Spec for R coffee-script

17 Updated Nov 26, 2013

Writing reviews of academic papers

499 106 Updated Aug 12, 2015

A multiplayer plugin for KMP

C# 140 49 Updated Aug 24, 2014

collection of small scripts or how-tos that don't fall under a separate project

Python 21 11 Updated Oct 18, 2017

RhythmBox plugin allowing to create playlist based on a Last.fm play log

Python 1 Updated Feb 10, 2012

RhythmBox plugin allowing to create playlist based on a Last.fm play log

Python 6 2 Updated Feb 14, 2012

Mirror of the new bioconductor svn for Repitools

R 3 Updated May 2, 2014

Tools for producing pseudo-cgh of next-generation sequencing data

Python 18 9 Updated Sep 5, 2016

GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and…

Python 1 1 Updated Jul 8, 2010

A git version of our Repitools R package (the R-forge svn version will *always* be more up do date)

R 3 Updated Jun 28, 2011

Alignment and Tabulation of BiSulfite Treated Reads

C 16 7 Updated Jan 7, 2014