philpalmer Goto Github PK

academia-hugo

antiviral-drug-repurposing

This side project was done for a PhD application research proposal as a proof of concept

attentive-parapred

Code for Attentive cross-modal paratope prediction

autoplate

RShiny app to automate the analysis of 96-well plates such as the fitting of dose-response curves for Pseduotype Micro Neutralisation (pMN) assays

biorisk-botecs

Back-of-the-envelope calculations (BOTECs) assessing different pandemic risks

biosecurity-trends

Analysis of trends in biosecurity

blog

My personal homepage built using the Hugo Academic Theme

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

cancer-prediction-pp502

companion

Pipeline for automatic eukaryotic parasite annotation

configs

Config files used to define parameters specific to compute environments at different Institutions

containers

Bioinformatics containers

cv

[LaTeX] My academic CV

cv-2

My curriculum vitae (CV) written using LaTeX.

data-downloader

Nextflow pipeline to download files using axel

deepvariant

Google's DeepVariant variant caller as a Nextflow pipeline

deepvariant-1

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

deepvirfinder

Identifying viruses from metagenomic data by deep learning

docker-impute2-1

docs

Notes for everything I know

dtc_genomics_convertor

A command line tool to go between 23andMe, AncestryDNA, and Family Tree DNA raw data formats.

eager2

WORK IN PROGRESS: Hopefully soon a fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.

ecw-converter

Dockerised python scripts & Nextflow pipeline for converting ecw files to either geotiffs or Cloud Optimised Geotiffs (COGs)

exome_depth_pipeline

A Bpipe pipeline for easily running ExomeDepth

exomedepth

Detects copy number variants in exomes and gene panels using high throughput DNA sequencing data

expansionhunter

expansionhunter-1

A tool for estimating repeat sizes

flowcraft-test

Testing pipeline built with flowcraft

freebayes

fullstack-nanodegree-vm