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14810 skills availablebio-genome-engineering-prime-editing-design
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions...
gene-database
NCBI Gene is a comprehensive database integrating gene information from diverse species. It provides nomenclature, refer...
bio-workflow-management-nextflow-pipelines
// main.nf nextflow.enable.dsl=2 params.reads = "data/{1,2}.fq.gz" params.outdir = "results" process FASTQC { input: tup...
bio-microbiome-functional-prediction
Reference examples tested with: Biostrings 2.70+, ggplot2 3.5+, pandas 2.2+, phyloseq 1.46+, scanpy 1.10+ Before using c...
vcf-statistics
Generate statistics and quality metrics using bcftools. | Command | Purpose | |---------|---------| | bcftools stats | C...
vcf-basics
View and query variant files using bcftools and cyvcf2. | Format | Description | Use Case | |--------|-------------|----...
variant-calling
Call SNPs and indels from aligned reads using bcftools. BAM file + Reference FASTA bcftools mpileup (generate pileup) bc...
variant-annotation
| Tool | Best For | Speed | Output | |------|----------|-------|--------| | bcftools csq | Simple consequence prediction...
joint-calling
Call variants jointly across multiple samples for improved accuracy and consistent genotyping. Improved sensitivity - Le...
gatk-variant-calling
GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workfl...
deepvariant
docker pull google/deepvariant:1.6.1 docker pull google/deepvariant:1.6.1-gpu singularity pull docker://google/deepvaria...
consensus-sequences
Apply variants to reference FASTA using bcftools consensus. bcftools consensus -f reference.fa input.vcf.gz > consensus....
clinical-interpretation
Prioritize and interpret variants for clinical significance using databases and ACMG/AMP guidelines. Annotated VCF ├── D...
ontology-validator
Validate that material sample annotations comply with ontology constraints: correct class names, valid properties, consi...
bio-chipseq-super-enhancers
Reference examples tested with: GenomicRanges 1.54+, bedtools 2.31+, ggplot2 3.5+, samtools 1.19+ Before using code patt...
bio-spatial-transcriptomics-spatial-communication
Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, squidpy 1.3+ Before using code ...
bio-clip-seq-clip-alignment
STAR --runMode alignReads \ --genomeDir STARindex \ --readFilesIn trimmed.fq.gz \ --readFilesCommand zcat \ --outFilterM...
bio-read-alignment-bwa-alignment
bwa-mem2 index reference.fa bwa-mem2 mem -t 8 reference.fa reads1.fq.gz reads2.fq.gz > aligned.sam bwa-mem2 mem -t 8 ref...
pptx
| Task | Guide | |------|-------| | Read/analyze content | python -m markitdown presentation.pptx | | Edit or create fro...
tooluniverse-clinical-trial-matching
Transform patient molecular profiles and clinical characteristics into prioritized clinical trial recommendations. Searc...
spatial-statistics
Compute spatial statistics and identify spatially variable features. import squidpy as sq import scanpy as sc import pan...
spatial-preprocessing
QC, filtering, normalization, and feature selection for spatial data. import squidpy as sq import scanpy as sc import nu...
spatial-multiomics
| Platform | Resolution | Spots/Beads | Coverage | |----------|------------|-------------|----------| | Visium | 55 µm |...
spatial-domains
Identify spatial domains and tissue regions by combining expression and spatial information. import squidpy as sq import...