In silico PCR command line tool for typing Escherichia coli ST131

Draw UpSet plots with Matplotlib

Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA

Code for our paper "Bayesian Mean-parameterized Nonnegative Binary Matrix Factorization"

NBMF-MM: Bernoulli Mean-Parameterized Non-negative Binary Matrix Factorization with Majorization-Minimization

SuperPrompt is an attempt to engineer prompts that might help us understand AI agents.

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

A list of interesting genome browser and genome visualization programs

Python package for analyzing and visualizing co-occuring gene / allele sets (phylons) within a pangenome

Easily migrate your codebase from one framework or language to another.

Automatically exported from code.google.com/p/cdhit

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.

Voilà turns Jupyter notebooks into standalone web applications

python Circos

PHANOTATE: a gene caller for phages.

⚡ ♒ Rapid prokaryotic genome annotation

Match IDs (or more precisely locus_tags) between two GenBank files.

Clermont PCR method In-Silico

📈 vue wrapper for plotly.js

Useful bash one-liners for bioinformatics.

Perl script to download genomes within a clade from NCBI Refseq

Parse GFF3 into Pandas dataframes

A collection of various notebook extensions for Jupyter

Uniform Manifold Approximation and Projection

Fast genome-wide functional annotation through orthology assignment

🆔 Scan contig files against PubMLST typing schemes

Files for the Genome Design/Genome Analytics Short-course organized by the SBRG