Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Frequently used commands in bioinformatics

A python package and a set of shell commands to handle GTF files

A digital scale to be integrated in furniture e.g. beds

Open-source toolkit that simplifies and speeds up work with bioinformatics data. high-perf-bio allows you easily upload VCF, BED or arbitrary tables to DB and execute popular bioinformatic queries without MongoDB Query Language knowledge.

A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton

A plugin to execute gcode commands when the print bed cools to a certain temperature

DRIP Optimized Peak Annotator

Extract coverage information from gVCF and variants from VCF files and output in tabular format.

Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.

Predicting Transcription Factor Binding Sites from ENCODE data using Machine Learning

Lightweight and memory efficient reader for PLINK BED files. It supports both SNP-major and individual-major formats. Written in Python.

Compare and shuffle heterozygosity using BED and VCF files

Fast intersection of sorted reference intervals

These scripts examine and display visual representations of .bedGraph and .bed files associated with CHIP-seq datasets.

Python implementation of the OpenGDC software https://github.com/cumbof/OpenGDC

Series of experiments on the BED dataset

This script annotates a BED file with gene information using the Ensembl REST API. It is specifically designed to work with human genome build GRCh37 (hg19).

ProOvErlap - Assessing feature proximity/overlap and testing statistical significance from genomic intervals