Package for fetching metadata and downloading data from SRA/ENA/GEO

Extension for 3D Slicer that allows the application to be used from Jupyter notebook

A basic introduction to Biopython, intended for a classroom based workshop

Python script to extract a STL surface from a DICOM image series.

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

a tool for designing primer panels for multiplex PCR.

Python bindings for the parasail C library.

This is a one-off Nextstrain build for SARS-like coronaviruses

A versatile sequenced read processor for nanopore direct RNA sequencing

This is a 3D Slicer extension for segmentation and spatial reconstruction of infiltrated, collapsed, and emphysematous areas in lung CT.

💻 GUI for creating bioinformatics workflows from 🐳 Docker containers:

Digital Pathology Whole Slide Image Analysis Toolbox

Clinical interpretation of somatic mutations in cancer

Malleable All-seeing Journal Of Research Artifacts

The Zika bioinformatics pipeline

Oxford Nanopore HDF/Fast5 to CRAM conversion tool

Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing

rapidly rid reads of horrid humans

Process consensus file for COG-UK data

Command line client and Python libraries for CosmosID API

DeepNovo workflow of neoantigen discovery by personalized de novo sequencing.

download sra files from SRA, pipe through fastq_dump and bowtie2 to S3, in a container

create an algorithm to identify metastatic cancer in small image patches taken from larger digital pathology scans

Makes the consensus sequence of sequences in a file

Code related to the Biobrick-directed Gibson assembly project

Script to generate OME-TIFF

Gibson Assembly mix calculator for molecular biology