FridrichMethod
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- ▌ Bio Read Alignment Hisat2 Alignment · fridrichmethod bundleAlign RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
- ▌ Bio Small Rna Seq Mirdeep2 Analysis · fridrichmethod bundleDiscover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data. Use when identifying new miRNAs or performing comprehensive miRNA profiling with discovery.
- ▌ Bio Small Rna Seq Target Prediction · fridrichmethod bundlePredict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally important miRNAs.
- ▌ Bio Workflows Metabolomics Pipeline · fridrichmethod bundleEnd-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.
- ▌ Bio Workflows Metagenomics Pipeline · fridrichmethod bundleEnd-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.
- ▌ Immune Checkpoint Combination Agent · fridrichmethodAI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular profiling.
- ▌ Alphafold Database Fetch And Analyze · fridrichmethod bundleRetrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.
- ▌ Bio Clip Seq Binding Site Annotation · fridrichmethod bundleAnnotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.
- ▌ Bio Data Visualization Genome Tracks · fridrichmethod bundleCreate genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tracks.
- ▌ Bio Experimental Design Batch Design · fridrichmethod bundleDesigns experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.
- ▌ Bio Expression Matrix Metadata Joins · fridrichmethod bundleMerge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.
- ▌ Bio Genome Intervals Bed File Basics · fridrichmethod bundleBED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.
- ▌ Bio Phasing Imputation Imputation Qc · fridrichmethod bundleQuality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputation accuracy before GWAS.
- ▌ Bio Read Alignment Bowtie2 Alignment · fridrichmethod bundleAlign short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
- ▌ Bio Small Rna Seq Differential Mirna · fridrichmethod bundlePerform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.
- ▌ Bio Workflows Crispr Screen Pipeline · fridrichmethod bundleEnd-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.
- ▌ Bio Workflows Expression To Pathways · fridrichmethod bundleWorkflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.
- ▌ Bio Data Visualization Color Palettes · fridrichmethod bundleSelect and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes. Use when selecting colorblind-friendly palettes for figures.
- ▌ Bio Expression Matrix Gene Id Mapping · fridrichmethod bundleConvert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.
- ▌ Bio Expression Matrix Sparse Handling · fridrichmethod bundleWork with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.
- ▌ Bio Genome Intervals Gtf Gff Handling · fridrichmethod bundleParse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.
- ▌ Bio Machine Learning Model Validation · fridrichmethod bundleImplements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets. Prevents data leakage and overfitting in biomarker discovery. Use when validating classifiers or optimizing hyperparameters on omics data.
- ▌ Bio Small Rna Seq Smrna Preprocessing · fridrichmethod bundlePreprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.
- ▌ Bio Systems Biology Gene Essentiality · fridrichmethod bundlePerform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding synthetic lethal drug targets.
- ▌ Bio Workflow Management Cwl Workflows · fridrichmethod bundleCreate portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.
- ▌ Bio Workflow Management Wdl Workflows · fridrichmethod bundleCreate 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.
- ▌ Bio Workflows Crispr Editing Pipeline · fridrichmethod bundleEnd-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.
- ▌ Bio Comparative Genomics Hgt Detection · fridrichmethod bundleDetect horizontal gene transfer events using HGTector, compositional analysis, and phylogenetic incongruence methods. Identify foreign genes in bacterial and archaeal genomes from anomalous composition or unexpected phylogenetic placement. Use when searching for horizontally transferred genes or analyzing genome evolution in prokaryotes.
- ▌ Bio Epitranscriptomics M6anet Analysis · fridrichmethod bundleDetect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immunoprecipitation.
- ▌ Bio Experimental Design Power Analysis · fridrichmethod bundleCalculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments. Use when planning experiments, determining how many replicates are needed, or assessing whether a study is adequately powered to detect expected effect sizes.
- ▌ Bio Genome Assembly Assembly Polishing · fridrichmethod bundlePolish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.
- ▌ Bio Genome Assembly Long Read Assembly · fridrichmethod bundleDe novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.
- ▌ Bio Genome Intervals Coverage Analysis · fridrichmethod bundleCalculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.
- ▌ Bio Machine Learning Omics Classifiers · fridrichmethod bundleBuilds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs. Includes proper preprocessing and evaluation metrics for biomarker classifiers. Use when building diagnostic or prognostic classifiers from expression or variant data.
- ▌ Bio Machine Learning Survival Analysis · fridrichmethod bundleAnalyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival models from clinical and omics features. Use when predicting patient survival or modeling time-to-event outcomes.
- ▌ Bio Rna Quantification Count Matrix Qc · fridrichmethod bundleQuality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.
- ▌ Bio Workflows Genome Assembly Pipeline · fridrichmethod bundleEnd-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.
- ▌ Bio Workflows Somatic Variant Pipeline · fridrichmethod bundleEnd-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.
- ▌ Bio Epitranscriptomics M6a Differential · fridrichmethod bundleIdentify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.
- ▌ Bio Epitranscriptomics M6a Peak Calling · fridrichmethod bundleCall m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.
- ▌ Bio Genome Assembly Metagenome Assembly · fridrichmethod bundleMetagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples.
- ▌ Bio Genome Assembly Short Read Assembly · fridrichmethod bundleDe novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads.
- ▌ Bio Phasing Imputation Reference Panels · fridrichmethod bundleDownload, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.
- ▌ Bio Experimental Design Multiple Testing · fridrichmethod bundleApplies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data. Use when filtering differential expression results, setting significance thresholds, or choosing between correction methods for different study designs.
- ▌ Bio Genome Intervals Interval Arithmetic · fridrichmethod bundleCore interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent intervals, or transferring annotations between interval files.
- ▌ Bio Machine Learning Biomarker Discovery · fridrichmethod bundleSelects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarkers from high-dimensional omics data.
- ▌ Bio Phasing Imputation Haplotype Phasing · fridrichmethod bundlePhase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes.
- ▌ Bio Rna Quantification Tximport Workflow · fridrichmethod bundleImport transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.
- ▌ Bio Comparative Genomics Synteny Analysis · fridrichmethod bundleAnalyze genome collinearity and syntenic blocks using MCScanX, SyRI, and JCVI for comparative genomics. Detect conserved gene order, chromosomal rearrangements, and whole-genome duplications. Use when comparing genome structure between species or identifying conserved genomic regions.
- ▌ Bio Data Visualization Multipanel Figures · fridrichmethod bundleCombine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels. Use when combining multiple plots into publication figures.
- ▌ Bio Genome Intervals Proximity Operations · fridrichmethod bundleFind nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter regions, or finding nearby genomic features.
- ▌ Bio Systems Biology Flux Balance Analysis · fridrichmethod bundlePerform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux distributions.
- ▌ Bio Workflows Metabolic Modeling Pipeline · fridrichmethod bundleEnd-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.
- ▌ Bio Data Visualization Heatmaps Clustering · fridrichmethod bundleCreate clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization. Use when visualizing expression patterns across samples or identifying co-expressed gene clusters.
- ▌ Bio Epitranscriptomics Merip Preprocessing · fridrichmethod bundleAlign and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
- ▌ Bio Phasing Imputation Genotype Imputation · fridrichmethod bundleImpute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, harmonizing data across genotyping platforms, or inferring variants not directly typed in array data.
- ▌ Bio Workflow Management Nextflow Pipelines · fridrichmethod bundleCreate 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.
- ▌ Bio Comparative Genomics Ortholog Inference · fridrichmethod bundleInfer orthologous gene groups across species using OrthoFinder and ProteinOrtho. Identify orthologs, paralogs, and co-orthologs for comparative genomics and functional annotation transfer. Use when identifying gene orthologs across species or building orthogroups for evolutionary analysis.
- ▌ Bio Comparative Genomics Positive Selection · fridrichmethod bundleDetect positive selection using dN/dS (omega) tests with PAML codeml and HyPhy. Identify sites and branches under adaptive evolution through codon models and branch-site tests. Use when testing for adaptive evolution in gene families or identifying positively selected sites.
- ▌ Bio Data Visualization Ggplot2 Fundamentals · fridrichmethod bundleCreate publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts. Use when creating static figures for papers, presentations, or reports in R.
- ▌ Bio Genome Assembly Contamination Detection · fridrichmethod bundleDetect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination.
- ▌ Bio Machine Learning Prediction Explanation · fridrichmethod bundleExplains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive classifier decisions. Use when interpreting biomarker classifiers or understanding model predictions.
- ▌ Bio Rna Quantification Alignment Free Quant · fridrichmethod bundleQuantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.
- ▌ Bio Systems Biology Context Specific Models · fridrichmethod bundleBuild tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.
- ▌ Bio Workflow Management Snakemake Workflows · fridrichmethod bundleBuild reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-based workflows, automating multi-step analyses with make-like dependency tracking, or running pipelines on HPC clusters with SLURM.
- ▌ Bio Data Visualization Volcano Customization · fridrichmethod bundleCreate publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib. Use when visualizing differential expression or association results with gene annotations.
- ▌ Bio Population Genetics Selection Statistics · fridrichmethod bundleDetect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics. Calculate population differentiation, test for departures from neutrality, and identify selective sweeps with scikit-allel and vcftools. Use when computing selection signatures like Fst or Tajima's D.
- ▌ Bio Systems Biology Metabolic Reconstruction · fridrichmethod bundleBuild genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis. Use when creating metabolic models for organisms without existing models.
- ▌ Bio Research Tools Biomarker Signature Studio · fridrichmethod bundleMulti-omic biomarker discovery studio that ingests expression + metadata, performs QC, multi-strategy feature selection, nested CV model training, survival analysis hooks, and SHAP-based interpretation. Use to design translational biomarker panels with documented evidence.
- ▌ Bio Rna Quantification Featurecounts Counting · fridrichmethod bundleCount reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.
- ▌ Bio Population Genetics Linkage Disequilibrium · fridrichmethod bundleCalculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLINK, scikit-allel, and LDBlockShow. Use when calculating LD or pruning variants.
- ▌ Bio Data Visualization Interactive Visualization · fridrichmethod bundleCreate interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations. Use when building zoomable, hoverable plots for data exploration or web dashboards.
- ▌ Bio Vcf Basics · fridrichmethod bundleView, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure.
- ▌ Bio Comparative Genomics Ancestral Reconstruction · fridrichmethod bundleReconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein resurrection or tracing evolutionary history.
- ▌ Bio Epitranscriptomics Modification Visualization · fridrichmethod bundleCreate metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons.
- ▌ Bio Variant Calling Deepvariant · fridrichmethod bundleDeep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller.
- ▌ Bio Variant Calling Joint Calling · fridrichmethod bundleJoint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping across multiple samples.
- ▌ Bio Vcf Statistics · fridrichmethod bundleGenerate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.
- ▌ Bio Variant Calling · fridrichmethod bundleCall SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
- ▌ Bio Vcf Manipulation · fridrichmethod bundleMerge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
- ▌ Bio Variant Annotation · fridrichmethod bundleComprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.