philippbayer Goto Github PK

followers: 186.0 following: 39.0 repos: 61.0 gists: 62.0

Name: Philipp Bayer

Type: User

Company: University of Western Australia

Bio: Using bioinformatics & interpretable AI to help the ocean at @MinderooFoundation OceanOmics

Twitter: philippbayer

Location: Perth, Australia

Blog: https://genomic.social/@PhilippBayer

Hi there 👋

I use computers to learn how genomes work.

🔭 I’m currently working on interpretable ML around environmental DNA (eDNA) from Western Australia's oceans. Hopefully soon I will have models which tell me which WA ocean areas are healthy, which areas show more diversity than expected, and which ones need help!
👯 I'm always happy to chat anything interpretable ML, especially applied to sequencing data (genomes/reads)!
📫 How to reach me: https://genomic.social/@philippbayer is probably fastest. if not, my Minderoo email is pbayerATminderooDOTorg
😄 Pronouns: he/him
💬 I regularly blog at https://philippbayer.github.io/blerg/
⚡ Fun fact: most crops we rely on (bread wheat, canola, coffee, cotton, strawberry, etc.) are allopolyploids, that means that their cells contain a bunch of genomes from two or more ancestral species (canola: 2 genomes, bread wheat: 3 genomes). We humans have only one genome, boring.

Philipp Bayer's Projects

machine_learning_notebooks

This is where I store Jupyter notebooks for machine learning/PMLG/Kaggle

matplotlib_tricks

Just a few matplotlib tricks because I keep on googling them

mendeley

A simple ruby wrapper for the mendeley api

oceanomics-amplicon

A pipeline to analyse marine fish amplicon data

oceanomics-classifier-comparison

Comparing eDNA taxonomic classifiers

oceanomics-enauploads

This keeps track of OceanOmics' ENA uploads; notably, the settings used and the returned statuses and IDs

opensnp28c3

The slides for our presentation of openSNP/personal genomics at the 28c3

orthomcltovenn

Creates Venn diagrams for OrthoMCL output

pasw-spss-parser

Just a small parser for the tab-delimited output of PASW

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

plt

A path to Programming Language Theory enlightenment

postdoc-funding-schemes

Funding schemes and opportunities for postdoc fellowships

qtlnetminer

QTLNetMiner is a platform for fast and systematic candidate gene discovery using data mining and network visualisation techniques

r-novice-gapminder

Introduction to R for non-programmers using gapminder data.

r_gene_analysis

Linking disease resistance gene numbers with yield in soybean

science_in_the_pursuit_of_a_trickster_god

submission_checklist

A checklist to help you avoid all those minor errors when submitting a scientific manuscript

supercharge_your_research_talk_1st_march_2023

A talk on my journey from regular biologist to data person

the_food_book_sandbox

This is a recipe book used to practice with Git, GitBook and GitHub

things-a-scientist-is-suppposed-to-know

A comprehensive and long list of things a modern scientist is supposed to know

Once upon a time, there was a bioinformatics summer project which involved the translation of HIV and SIV nucleotide sequences. It was for @gedankenstuecke and me the first time we coded for longer than 5 lines. This is it. Warning: It's terrible.

wrangling-pangenomes

Data Wrangling and Processing for pangenomics

philippbayer Goto Github PK

Hi there 👋

Philipp Bayer's Projects

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