MatthiasZepper
Computational biologist experienced in analyzing massive parallel sequencing data. Leveraging software for life science @NationalGenomicsInfrastructure
@SciLifeLabStockholm
Pinned Repositories
beamer-scilifelab
A modern LaTeX Beamer theme
gh-api-confine
A Github action step to query the remaining Github API limit and rescind or pause a workflow run.
impftermincheck
Automatisierte Überprüfung, ob im Impfzentrum der Wahl noch Termine verfügbar sind
Lecture-OmicsDataAnlysis
Introductionary lecture on genomics data analysis.
LimaVM_nf-core_apptainer
A virtual machine for Lima to run nf-core/Nextflow/Apptainer on a macOS host.
linux-portfolio
Personal portfolio website of theme Ubuntu 20.04, made using NEXT.js & tailwind CSS
nf-core-statistics
A Github Action to gather Github stats about an organization. Written by Harrison Hogg for Spotify Backstage and slightly adapted to nf-core.
thesis
My PhD thesis: Epigenetic characterization of murine Dnmt1-deficient MLL-AF9 leukemia
whisper-dockerized
A Docker image of OpenAI's Whisper model for advanced speech recognition.
umi-transfer
A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.
MatthiasZepper's Repositories
MatthiasZepper/LimaVM_nf-core_apptainer
A virtual machine for Lima to run nf-core/Nextflow/Apptainer on a macOS host.
MatthiasZepper/nf-core-statistics
A Github Action to gather Github stats about an organization. Written by Harrison Hogg for Spotify Backstage and slightly adapted to nf-core.
MatthiasZepper/whisper-dockerized
A Docker image of OpenAI's Whisper model for advanced speech recognition.
MatthiasZepper/gh-api-confine
A Github action step to query the remaining Github API limit and rescind or pause a workflow run.
MatthiasZepper/Lecture-OmicsDataAnlysis
Introductionary lecture on genomics data analysis.
MatthiasZepper/bamtofastq
Converts bam or cram files to fastq format and does quality control.
MatthiasZepper/dds_cli
API to access Scilifelab Data Centre's delivery portal. On development
MatthiasZepper/dds_web
A cloud-based system for the delivery of data from SciLifeLab Facilities to their users (e.g. research group).
MatthiasZepper/imgpilot
Turn the draft into amazing artwork with the power of Real-Time Latent Consistency Model
MatthiasZepper/modkit
A bioinformatics tool for working with modified bases
MatthiasZepper/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
MatthiasZepper/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
MatthiasZepper/MultiQC-testdata
Test data for MultiQC.
MatthiasZepper/Nextflow_withLabel_prio
A small Nextflow test pipeline to establish the selector priority for multiple withLabel selectors.
MatthiasZepper/nf-core-website
Code and files for the main nf-core website.
MatthiasZepper/nf-core_seqinspector
QC pipeline to inspect your sequences
MatthiasZepper/nfcore-testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.
MatthiasZepper/ngisweden.se
Wordpress theme and plugins for ngisweden.se
MatthiasZepper/paolos-awesome-pipeline
A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin
MatthiasZepper/paper-qa
LLM Chain for answering questions from documents with citations
MatthiasZepper/perbase
Per-base per-nucleotide depth analysis
MatthiasZepper/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
MatthiasZepper/rumidup
UMI aware mark (optical) duplicates in NGS sequencing BAM
MatthiasZepper/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
MatthiasZepper/seqeralabs-tower-agent
Agent app that allows connecting remote batch schedulers to Tower Cloud
MatthiasZepper/stargazer
Your repo reached a stars milestone? Celebrate with a video of your stargazers!
MatthiasZepper/tools
Python package with helper tools for the nf-core community.
MatthiasZepper/twkit
BETA: Python implementation for automated pipeline launching through Tower CLI
MatthiasZepper/umi-transfer
A Rust software to extract Unique Molecular Identifiers in FastQ files and embedd them into the ID of the corresponding reads.
MatthiasZepper/VerbaExtended
Retrieval Augmented Generation (RAG) chatbot powered by Weaviate