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
blockchain scientific computing AI Skills
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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
GitHub
bio-restriction-fragment-analysis
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
☆ 299View skill
GitHub
bio-metagenomics-strain-tracking
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, tra...
☆ 299View skill
GitHub
bio-chipseq-differential-binding
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values.
☆ 299View skill
GitHub
bio-workflows-proteomics-pipeline
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma.
☆ 299View skill
GitHub
bio-pdb-structure-navigation
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use for accessing models, chains, residues, and atoms, iterating over structure levels, extracting sequences, identifying residue types,...
☆ 299View skill
GitHub
bio-data-visualization-genome-tracks
Create 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 tra...
☆ 299View skill
GitHub
bio-chipseq-visualization
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions.
☆ 299View skill
GitHub
bio-read-alignment-star-alignment
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Use for RNA-seq data requiring splice-aware alignment. Supports two-pass mode for novel splice junction discovery.
☆ 299View skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 283View skill
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