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linsnap

Screenshot taking and management tool.

machinelearning

Experimentation with machine learning algorithms such as K Nearest Neighbours, Support Vector Machines and Neural Networks.

macs

MACS -- Model-based Analysis of ChIP-Seq

makechains

Chain file generation script for Mammouth cluster.

mastering-shiny

Mastering Shiny: a book

mineserver

Minecraft server manager.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

nanovar

Structural variant caller for low-depth long-read sequencing data

nearestpaths

Find nearest paths in a genome graph

nextflow_scripts

pangenie_nextflow

Nextflow script to run PanGenie on thousands of samples.

panmethyl

Map Pacbio methylation data to genome graphs.

personalized_genomes_gbio

pggb

the pangenome graph builder

qls_li_lab

qlsc600-odes

qlsc600_m2a2

GWAS on admixed populations

qlsc_m4a2

qq_plot_gg

qqplot with ggplot

repeatr

read and analyse RepeatMasker output

sane-mmtag

Program that parses base modifications data in BAM files and outputs read annotations in sane BED-like coordinates.

seqalign

Experimentation with bioinformatics.

seqlib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

smoothxg

linearize and simplify variation graphs using blocked partial order alignment

sv_segway

svaba

Structural variation and indel detection by local assembly

templates

Repository to store templates for Markdown, Org, Latex etc ...

twauctex

Tweaks for AUCtex

ultrabubble_paths

Function to work with ultrabubble paths in vg graphs.

vcf2diploid

personal genome constructor