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atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

bin-sim-meas

Various scripts form simulating biases in binary similarity measures

bionumpy-example-data

Example data for BioNumPy

bionumpy_snp_kmer_filtering_example

bios3010-python

Exercises and teaching material for the Python part of bios3010

chipulate

A Python3 framework to simulate read counts in a ChIP-seq experiment.

complete-striped-smith-waterman-library

copilot_testproject

cov_sequences

SARS-CoV-2 genome from Nigeria

cruzdb

python access to UCSC genomes database

deep

Compare two nested Python data structure and pinpoint the first place they differ

fastqc

A quality control analysis tool for high throughput sequencing data

genotyping-benchmarking

Snakemake-pipeline for benchmarking genotypers

graph_kmer_index

Simple python kmer index for graphs

graph_read_simulator

Simple diploid read simulator using genome graphs

hic-assembly-benchmarking

hierarchical_results

Simple test of a hierarchical disk-backed logger

in1000-crafts-public

infra-api

Api for infrastructure server (for github-hooks)

javascript-winwheel

Create spinning prize wheels on HTML canvas with Winwheel.js

kage-indexing

Snakemake pipeline for creating indexes for the KAGE genotyper

kage2-manuscript

kmer_mapper

Simple numpy/cython based kmer mapper for mapping kmers from a fasta file to an index

obgraph

Simple offsetbased graph implementation using Numpy

open-the-lid-chip-seq-analysis

Scripts and guide for reproducing the ChIP-seq analysis in Open the LID: LXRα regulates ChREBPα transactivity in a target gene-specific manner through an agonist-modulated LBD-LID interaction

paragraph

Graph realignment tools for structural variants

privvg-challenge

python-bioinformatics

Modules for Python in bioinformatics

pythontest

Pythontest

qmlgalaxyportal

A mobile QML app for interfacing with the Galaxy API