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shap
SHAP is a unified approach to explain machine learning model outputs using Shapley values from cooperative game theory. This skill provides comprehens...
bio-genome-intervals-bed-file-basics
BED (Browser Extensible Data) format stores genomic intervals. Uses 0-based, half-open coordinates. BED3: chr start end BED4: chr start end nam...
geopandas
GeoPandas extends pandas to enable spatial operations on geometric types. It combines the capabilities of pandas and shapely for geospatial data analy...
bio-data-visualization-color-palettes
| Type | Use Case | Example | |------|----------|---------| | Sequential | Continuous data (expression, coverage) | viridis, Blues | | Diverging | Cen...
docx-official
A user may ask you to create, edit, or analyze the contents of a .docx file. A .docx file is essentially a ZIP archive containing XML files and other ...
test-driven-development
Write the test first. Watch it fail. Write minimal code to pass. Core principle: If you didn't watch the test fail, you don't know if it tests the rig...
bio-copy-number-gatk-cnv
Reference examples tested with: GATK 4.5+ Before using code patterns, verify installed versions match. If versions differ: CLI: <tool> --version then ...
pdf-processing
Use pdfplumber to extract text from PDFs: import pdfplumber with pdfplumber.open("document.pdf") as pdf: text = pdf.pages[0].extracttext() print(text)...
bio-ribo-seq-riboseq-preprocessing
Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, cutadapt 4.4+, numpy 1.26+, pysam 0.22+, samtools 1.19+ Before using code patterns, veri...
matchms
Matchms is an open-source Python library for mass spectrometry data processing and analysis. Import spectra from various formats, standardize metadata...
bio-phasing-imputation-imputation-qc
bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%INFO/DR2\t%INFO/AF\n' \ imputed.vcf.gz > infoscores.txt bcftools query -f '%CHROM\t%POS\t%ID\t%REF\...
bio-small-rna-seq-target-prediction
miranda miRNA.fa UTRs.fa \ -sc 140 \ -en -20 \ -out predictions.txt import pandas as pd def parsemiranda(outputfile): '''Parse miRanda output file''' ...