GitHub
bio-local-blast
Run local BLAST searches using BLAST+ command-line tools. Use for fast unlimited searches, custom databases, large-scale analysis, and when NCBI servers are slow or unavailable.
☆ 299View skill
databases bioinformatics AI Skills
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GitHub
bio-metagenomics-functional-profiling
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when you need pathway abundances, gene family counts, or functional annotations from metagenomic data.
☆ 299View skill
GitHub
bio-expression-matrix-counts-ingest
Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.
☆ 299View skill
GitHub
bio-data-visualization-interactive-visualization
Create 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 dashboard...
☆ 299View skill
GitHub
bio-hi-c-analysis-hic-visualization
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures.
☆ 299View skill
GitHub
bio-proteomics-protein-inference
Protein grouping and inference from peptide identifications. Handles shared peptides, protein groups, and protein-level FDR control using parsimony and probabilistic approaches.
☆ 299View skill
GitHub
bio-genome-assembly-contamination-detection
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies.
☆ 299View skill
GitHub
bio-expression-matrix-gene-id-mapping
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when you need to map IDs for pathway analysis or to match different data sources.
☆ 299View skill
GitHub
bio-longread-qc
Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio...
☆ 299View skill
GitHub
bio-sam-bam-basics
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.
☆ 299View skill
GitHub
bio-sequence-similarity
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use for identifying orthologs, distant homologs, and protein family members when standard BLA...
☆ 299View skill
GitHub
bio-chipseq-peak-calling
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats inc...
☆ 299View skill
GitHub
bio-alignment-pairwise
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use for comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DN...
☆ 299View skill
GitHub
bio-atac-seq-atac-peak-calling
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
☆ 299View skill
GitHub
bio-pathway-go-enrichment
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Tests whether GO terms are enriched in a gene list compared to background. Supports all three ontologies (BP, MF, CC), multiple ID type...
☆ 299View skill
GitHub
bio-methylation-calling
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite...
☆ 299View skill
GitHub
bio-workflows-fastq-to-variants
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller.
☆ 299View skill
GitHub
bio-sequence-statistics
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
☆ 299View skill
GitHub
bio-variant-annotation
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance.
☆ 299View skill
GitHub
bio-genome-assembly-hifi-assembly
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully reso...
☆ 299View skill
GitHub
bio-workflows-expression-to-pathways
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
☆ 299View skill
GitHub
bio-database-access-uniprot-access
Access UniProt protein database for sequences, annotations, and functional information. Use when you need protein data, GO terms, domain annotations, or protein-protein interactions.
☆ 299View skill
GitHub
bio-copy-number-cnv-annotation
Annotate CNVs with genes, pathways, and clinical significance. Use to interpret CNV calls and identify affected genes.
☆ 299View skill
GitHub
bio-proteomics-spectral-libraries
Build, manage, and search spectral libraries for proteomics. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
☆ 299View skill
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