albert-ying/autonomous-lab
21 skills · 1 total installs
$npx skills add albert-ying/autonomous-labSkillInstalls
scanpySingle-cell RNA-seq analysis with Scanpy. QC, normalization, clustering, visualization, marker gene identification.brackenUse Bracken to estimate species/genus/phylum-level abundances from Kraken2 classification results.bwa-mappingUse when mapping paired-end or single-end sequencing reads to a reference genome.bwa-mem2Use for aligning paired-end Illumina reads to a reference genome. BWA-MEM2 is the successor to BWA-MEM with improved performance.comparative-genomicsUse for comparing gene content, synteny, and functional modules across genomes.differential-expressionDifferential gene expression analysis with PyDESeq2. Design matrices, contrasts, multiple testing correction, volcano plots.kallistoUse Kallisto as an alternative to Salmon for transcript-level quantification from RNA-Seq reads using pseudoalignment.kraken2Use Kraken2 for taxonomic classification of metagenomic sequencing reads against a reference database.metagenomics-analysisUse for end-to-end metagenomic community profiling from raw reads to taxonomic abundance tables.orthofinderUse OrthoFinder for identifying orthologous gene groups across multiple genomes, inferring gene trees, and identifying orthogroups (clusters of orthologous…phylogeneticsUse for phylogenetic tree reconstruction from sequence alignments.prodigalUse Prodigal for ab initio gene prediction in prokaryotic genomes.salmonUse Salmon for fast, accurate transcript-level quantification from RNA-Seq reads.samtoolsUse for BAM/SAM file manipulation, sorting, indexing, and basic variant calling support.scientific-analysis-reviewCritically review AI-agent-conducted scientific analyses for correctness, rigor, and completeness.single-cell-rna-seqEnd-to-end single-cell RNA-seq analysis including data loading, QC, integration, clustering, cell type annotation, and differential expression.snpeffUse for annotating variants with gene names, functional effects, and impact predictions.snpeff-annotationUse when annotating variants with functional impact predictions (gene, effect, impact).spades-assemblyUse for de novo genome assembly when no reference genome is available.trimmomaticUse Trimmomatic to trim adapter sequences and low-quality bases from Illumina sequencing reads.variant-callingUse when calling SNPs and indels from aligned BAM files against a reference.