Silas Kieser's repositories
Snaketool
Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff
CMMG_tools
Code for analysis of CMMG
scikit-bio
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
scikit-bio-feedstock
A conda-smithy repository for scikit-bio.
snakemake-workflow-template
A template for standard compliant snakemake-workflows
dbcan
dbcan V3, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
curatedMetagenomicDataCuration
Sample Metadata Curation for curatedMetagenomicData
scanpy
Single-cell analysis in Python. Scales to >1M cells.
curatedMetagenomicDataAnalyses
Analyses in R and Python Using curatedMetagenomicData
anadama2
AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to capture your workflow and execute it efficiently on your local machine or in a grid compute environment (ie. sun grid engine or slurm).
vamb
Variational autoencoder for metagenomic binning
WarmMicrobiota
Code and supplementary data
academic-pandoc-template
Write beautiful academic texts with the distraction-free Pandoc Markdown.
FunMetagenomics
Genome-resolved functional metagenomics for human and mice
microbiome-analysis
CODA microbiome-analysis using aldex2, pylofactorisation
clusterprofile_hmi
Snakemake profile for cluster submission of Atlas on almost any cluster system
phd-thesis-template
A LaTeX / XeLaTeX / LuaLaTeX PhD thesis template for Cambridge University Engineering Department (CUED)
iMGMC
Repository of the integrated mouse gut metagenomic catalog
enrichM
Toolbox for comparative genomics of MAGs
academic-kickstart
📝 Easily create a beautiful website using Academic, Hugo, and Netlify
pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
table2itol
Generating iToL annotations from Spreadsheet or CSV files
viralVerify
viralVerify: viral contig verification tool
drep
Rapid comparison and dereplication of genomes
SCAPP
SCAPP is a plasmid assembly tool. A preprint describing this tool is available at: https://www.biorxiv.org/content/10.1101/2020.01.12.903252v1