DevOps & Infra

fridrichmethod Bundle

End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization. Use when processing Hi-C data to compartments and TADs.

fridrichmethod Bundle

End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.

fridrichmethod Bundle

End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.

fridrichmethod Bundle

Nature Literature Pipeline

fridrichmethod Bundle

End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods.

fridrichmethod Bundle

End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.

fridrichmethod Bundle

End-to-end MeRIP-seq analysis from FASTQ to m6A peaks and differential methylation. Use when analyzing epitranscriptomic m6A modifications from immunoprecipitation data.

fridrichmethod Bundle

End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.

fridrichmethod Bundle

End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.

fridrichmethod Bundle

End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.

fridrichmethod Bundle

End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy. Use when analyzing spatial transcriptomics data.

fridrichmethod Bundle

End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.

fridrichmethod Bundle

End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.

fridrichmethod Bundle

End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.

fridrichmethod Bundle

End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.

fridrichmethod Bundle

Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression.

fridrichmethod Bundle

End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.

fridrichmethod Bundle

End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma. Use when processing mass spectrometry proteomics.

fridrichmethod Bundle

End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.

fridrichmethod Bundle

End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.

fridrichmethod Bundle

End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics datasets.

fridrichmethod Bundle

End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping. Use when processing LC-MS metabolomics data.

fridrichmethod Bundle

End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.

fridrichmethod Bundle

End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods. Use when analyzing pooled CRISPR screens from count data to hit calling.

fridrichmethod Bundle

Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GATK best practices pipelines, working with Terra/AnVIL platforms, or building workflows for cloud execution on Google Cloud or AWS.

fridrichmethod Bundle

End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.

fridrichmethod Bundle

End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.

fridrichmethod Bundle

End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics. Use when calling somatic mutations from tumor-normal pairs.

fridrichmethod Bundle

End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or predicting metabolic phenotypes from genomic data.

fridrichmethod Bundle

Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on cloud platforms (AWS, Google Cloud), or leveraging nf-core community pipelines.

mittuled Bundle

This skill manages the investor relationship pipeline including tracking, nurturing, and prioritization. Use when asked to maintain the investor CRM, prioritize investor outreach, or track relationship status. Also consider when preparing for a future fundraise and needing to build relationships early. Suggest when the user is approaching investors without pipeline tracking.

mittuled Bundle

This skill analyses the full revenue funnel from lead to renewal to identify conversion bottlenecks. Use when asked to diagnose pipeline health, identify conversion drops, or forecast revenue. Also consider when win rates decline without a clear cause. Suggest when quarterly planning needs data-driven pipeline insights.

mittuled Bundle

This skill manages the fundraising process including investor pipeline, diligence coordination, and term sheet negotiation support. Use when asked to run a fundraise, manage investor outreach, or coordinate due diligence. Also consider when the company is 6 months from needing capital and should begin fundraising preparation. Suggest when the user is approaching investors without a structured process.

mittuled Bundle

This skill scales revenue operations infrastructure to support growing pipeline and customer volume. Use when asked to handle RevOps growing pains, optimise workflows for higher volume, or plan infrastructure capacity. Also consider when manual processes are breaking under increased deal flow. Suggest when pipeline volume doubles and existing processes show strain.

mittuled Bundle

Builds reliable CI/CD pipelines that turn every commit into a deployable, tested artifact. Use when asked to ci cd pipeline builder. Suggest when relevant.

mittuled Bundle

Lays the secure, well-structured cloud foundation that every service and team will build on. Use when asked to cloud foundation setup. Suggest when relevant.