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Tom Stanton (tomdstanton)

tomdstanton

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Company:Monash University

Location:Melbourne

Home Page:https://wyreslab.com/team/

Twitter:@tomstantonmicro

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Tom Stanton's starred repositories

polars

Dataframes powered by a multithreaded, vectorized query engine, written in Rust

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python-fire

Python Fire is a library for automatically generating command line interfaces (CLIs) from absolutely any Python object.

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BioGPT

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timevis

📅 Create interactive timeline visualizations in R

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Sniffles

Structural variation caller using third generation sequencing

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pgap

NCBI Prokaryotic Genome Annotation Pipeline

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fastq-dl

Download FASTQ files from SRA or ENA repositories.

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skani

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

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block-aligner

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

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pyhmmer

Cython bindings and Python interface to HMMER3.

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parasail-python

Python bindings for the parasail C library.

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r3dmol

🧬 An R package for visualizing molecular data in 3D

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inphared

Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.

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minimap2-rs

Rust bindings to minimap2 library

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WIsH

Predict prokaryotic host for phage metagenomic sequences

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mm2-fast

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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NGLVieweR

Visualize and interact with Protein Data Bank (pdb) and structural files in R and Shiny

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Scrooge

Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improvements on top of GenASM, and high-performance CPU and GPU implementations. Described by Lindegger et al. at https://doi.org/10.48550/arXiv.2208.09985

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SVbyEye

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deidentifyr

👥 An R package for deidentifying datasets that may contain personally identifiable information (PII)

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pyskani

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

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seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

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marvis

VMD Audio/Text control with natural language

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alignment-chart

Repository for R-driven ali{g}nment char{t}s

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bact-gen-scripts

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Spyder

Automatic robot for web scraping data from Pathogen Watch website using a RESTful API and MongoDB to store and manage the scraped data.

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bioinf-scripts

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phyloworkshop_2017

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GRRpair

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SeqDepth

Calculate sequencing depth of Illumina short-reads

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