jfy133
Bioinformatician with specialism in ancient DNA and metagenomics. nf-core core-team member and SPAAM community founder. @jfy133@genomic.social
HKI Jena, MPI-EVA LeipzigLeipzig, Germany
Pinned Repositories
archaeodiet
[Under constrution] Pipeline for metagenomic identification and authentication of ancient dietary DNA from archaeological samples
cuperdec
R library to generate 'Cumulative Percent Decay' curves for microbial taxonomic profiles
Hominid_Calculus_Microbiome_Evolution
Additional supplementary information and code, data repository for Fellows Yates, J.A. et al. (2021) PNAS. DOI: http://dx.doi.org/10.1073/pnas.2021655118
MEx-IPA
Interactive results viewer for maltExtract
nf-core-nft-utils
nf-test utility functions
rma-tabuliser
Bash wrapper script to generate count/taxon/OTU tables from RMA6 files (wrapper to MEGAN6 rma2info)
Tidy_PopGen_PCA_Plotting
A small R notebook describing how plot common (aDNA) population genetics PCAs using R and the tidyverse.
eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
AncientMetagenomeDir
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
jfy133's Repositories
jfy133/nf-core-nft-utils
nf-test utility functions
jfy133/nf-core-logos
Host nf-core logos and templates for making new logos
jfy133/nf-core-tools
Python package with helper tools for the nf-core community.
jfy133/bergstrom2024comment
Data and plot generation for Bergström, Fellows Yates and Warinner 2024
jfy133/acad-workshop-2024
Command's from Mikkel's github sessiopn at ACAD aeDNA workshop
jfy133/AncientMetagenomeDir
Repository containing lists of all published ancient metagenome samples (and related)
jfy133/askimed-nf-test
Simple test framework for Nextflow pipelines
jfy133/bioconda-bioconda-docs
Documentation for bioconda
jfy133/bioconda-recipes
Conda recipes for the bioconda channel.
jfy133/configBuilder-nf
Nextflow config builder scripts for supported HPC infrastructures.
jfy133/dotfiles
Personal dotfiles
jfy133/effective-doodle
jfy133/genomics-standards-consortium-mixs
Minimum Information about any (X) Sequence” (MIxS) specification
jfy133/jfy133
jfy133/jfy133.github.io
jfy133/multi-package-containers
Testing building mulled containers for multi-requirement tools.
jfy133/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
jfy133/nextflow-io-nextflow
A DSL for data-driven computational pipelines
jfy133/nf-core-configs
Config files used to define parameters specific to compute environments at different Institutions
jfy133/nf-core-funcscan
Screening of functional components and natural products from assembled contigs
jfy133/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
jfy133/nf-core-test-datasets
Test data to be used for automated testing with the nf-core pipelines
jfy133/nf-core-website
Code and files for the main nf-core website.
jfy133/pathPhynder
A workflow for integrating ancient lineages into present-day phylogenies.
jfy133/quarto-quarto-web
Quarto website
jfy133/special-barnacle
jfy133/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
jfy133/summerschool-github-practise
Empty repository for practising GitHub forking and pull requests
jfy133/taxprofiler-manuscript
Repository of Quarto version of nf-core/taxprofiler manuscript
jfy133/ubinfie-blog
µbinfie blog