A SingleCell RNASeq pre-processing snakemake workflow

AlphaFold-based Protein Analysis Pipeline

A miniature example of a MultiQC plugin.

MultiQC plugin for the National Genomics Infrastructure in Stockholm, Sweden.

MultiQC plugin dedicated to interact and analyze neuroimaging outputs.

Estimate fastq-formatted read abundace in RNA-Seq analysis with Kallisto

Map and post-process your bams for SNP calling

A Snakemake-based pipeline for processing and quality-controlling ancient DNA data, including contamination assessment and comparative genomic analysis across time points, producing damage-rescaled, mapped reads ready for downstream analyses.

A workflow automation script: demultiplex the library sequence, run quality checks, deliver to processing and archiving to NIRD

ORACLE RNA-seq pipeline — STAR + DESeq2 + GSEA, multi-species, metadata-driven design

Professional MCP server for FastQC and MultiQC quality control analysis with advanced visualization and report parsing

A Snakemake workflow for quality control assessment of Illumina NGS data using FastQC and MultiQC

Snakemake workflow for Salmon quantification and FastQC quality controls

MultiQC plugin interacting with the Illumina Genologics Clarity LIMS

Additional MultiQC report sections for 10x Genomics Xenium data.

CCBR pipeline for preliminary QC, peak calling, differential chromatin accessibility analysis with ATACseq datasets 🌲

ORACLE histone ChIP-seq pipeline (Snakemake): QC, Bowtie2, MACS2 broad peaks, DiffBind differential binding, monaLisa/JASPAR motifs, deepTools, MultiQC (human/mouse/rat).

Bioinformatics workflow platform skeleton with FastAPI, PostgreSQL metadata tracking, and a minimal Nextflow DSL2 FastQC/MultiQC QC workflow.

A Snakemake Workflow for using PolyA_DB and UCSC LiftOver with CellRanger

Execution-capable genomics workflow agent for reproducible NGS QC, variant-QC, nf-core orchestration, provenance, and agentic reporting.