GitHub
bio-variant-calling-deepvariant
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
☆ 300View skill
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bio-population-genetics-scikit-allel-analysis
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structu...
☆ 300View skill
GitHub
bio-pdb-geometric-analysis
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use for measuring distances, angles, and dihedrals, finding neighbor atoms, superimposing structures, calculating RMSD, identifying...
☆ 300View skill
GitHub
bio-population-genetics-selection-statistics
Detect 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 sweep...
☆ 300View skill
GitHub
bio-de-edger-basics
Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estim...
☆ 300View skill
GitHub
bio-primer-design-primer-validation
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability.
☆ 300View skill
GitHub
bio-hi-c-analysis-hic-data-io
Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats.
☆ 300View skill
GitHub
bio-sequence-properties
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.
☆ 300View skill
GitHub
bio-genome-intervals-coverage-analysis
Calculate 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 sequencin...
☆ 300View skill
GitHub
bio-motif-search
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme a...
☆ 300View skill
GitHub
bio-spatial-transcriptomics-spatial-data-io
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates.
☆ 300View skill
GitHub
bio-basecalling
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado or Guppy basecallers. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when proces...
☆ 300View skill
GitHub
bio-hi-c-analysis-tad-detection
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure.
☆ 300View skill
GitHub
bio-metabolomics-lipidomics
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classe...
☆ 300View skill
GitHub
bio-pdb-structure-modification
Modify protein structures using Biopython Bio.PDB. Use for transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, renumbering residues, and building stru...
☆ 300View skill
GitHub
bio-workflows-metabolomics-pipeline
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping.
☆ 300View skill
GitHub
bio-metabolomics-targeted-analysis
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves a...
☆ 300View skill
GitHub
bio-pdb-structure-io
Parse and write protein structure files using Biopython Bio.PDB. Use for reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, extracting header information, and writing structures to variou...
☆ 300View skill
GitHub
bio-metabolomics-msdial-preprocessing
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis...
☆ 300View skill
GitHub
bio-metabolomics-metabolite-annotation
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untarget...
☆ 300View skill
GitHub
bio-proteomics-ptm-analysis
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic...
☆ 300View skill
GitHub
bio-crispr-screens-hit-calling
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen cou...
☆ 300View skill
GitHub
bio-workflows-cnv-pipeline
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
☆ 300View skill
GitHub
bio-imaging-mass-cytometry-spatial-analysis
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for...
☆ 300View skill
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