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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use for comparing alignment quality, measuring sequence divergence, and analyzing...
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE em...
Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices.
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps.
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps,...
Run remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use for sequence similarity searches, identifying unknown sequences, finding homologs, and querying NCBI's nr/nt databases.
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
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...
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...
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...
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...
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability.
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.
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.
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...
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...
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.
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...
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure.
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...
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping.
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic...
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...
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
Le classement utilise les étoiles du dépôt GitHub indexé. Plusieurs skills peuvent partager ce nombre : ce n’est ni un nombre d’installations ni une note de qualité.