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14810 skills availablebio-phylo-modern-tree-inference
Build maximum likelihood phylogenetic trees with automatic model selection and ultrafast bootstrap. iqtree2 -s alignment...
bio-phasing-imputation-haplotype-phasing
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar java -jar beagle.22Jul22.46e.jar \ gt=input.v...
bio-pdb-structure-modification
Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match...
bio-pathway-wikipathways
Reference examples tested with: ReactomePA 1.46+, clusterProfiler 4.10+, rWikiPathways 1.24+ Before using code patterns,...
bio-pathway-reactome
Reference examples tested with: R stats (base), ReactomePA 1.46+, clusterProfiler 4.10+ Before using code patterns, veri...
bio-pathway-kegg-pathways
Reference examples tested with: R stats (base), clusterProfiler 4.10+ Before using code patterns, verify installed versi...
bio-pathway-go-enrichment
Reference examples tested with: R stats (base), clusterProfiler 4.10+ Before using code patterns, verify installed versi...
bio-multi-omics-similarity-network
Reference examples tested with: scanpy 1.10+ Before using code patterns, verify installed versions match. If versions di...
bio-multi-omics-mofa-integration
Reference examples tested with: scanpy 1.10+ Before using code patterns, verify installed versions match. If versions di...
bio-multi-omics-mixomics-analysis
Reference examples tested with: mixOmics 6.26+ Before using code patterns, verify installed versions match. If versions ...
bio-multi-omics-data-harmonization
Reference examples tested with: DESeq2 1.42+ Before using code patterns, verify installed versions match. If versions di...
bio-microbiome-taxonomy-assignment
Reference examples tested with: DADA2 1.30+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+ Before usin...
bio-microbiome-qiime2-workflow
Reference examples tested with: DADA2 1.30+, MAFFT 7.520+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1....
bio-microbiome-diversity-analysis
Reference examples tested with: R stats (base), ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+, vegan 2.6+ Before using code...
bio-microbiome-differential-abundance
Reference examples tested with: DESeq2 1.42+, ggplot2 3.5+, phyloseq 1.46+, scanpy 1.10+ Before using code patterns, ver...
bio-methylation-dmr-detection
Reference examples tested with: GenomicRanges 1.54+ Before using code patterns, verify installed versions match. If vers...
bio-methylation-calling
Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions dif...
bio-methylation-bismark-alignment
Reference examples tested with: Bowtie2 2.5.3+, HISAT2 2.2.1+, Trim Galore 0.6.10+, samtools 1.19+ Before using code pat...
bio-methylation-based-detection
Reference examples tested with: Bismark 0.24+, numpy 1.26+, pandas 2.2+, pysam 0.22+, scipy 1.12+, statsmodels 0.14+ Bef...
bio-metagenomics-visualization
Reference examples tested with: MetaPhlAn 4.1+, ggplot2 3.5+, matplotlib 3.8+, pandas 2.2+, phyloseq 1.46+, scanpy 1.10+...
bio-metagenomics-strain-tracking
Reference examples tested with: Bowtie2 2.5.3+, MetaPhlAn 4.1+, numpy 1.26+, pandas 2.2+, samtools 1.19+, scipy 1.12+ Be...
bio-metagenomics-metaphlan
Reference examples tested with: Bowtie2 2.5.3+, MetaPhlAn 4.1+, minimap2 2.26+, pandas 2.2+, scanpy 1.10+ Before using c...
bio-metagenomics-kraken
Reference examples tested with: Kraken2 2.1+, MetaPhlAn 4.1+, pandas 2.2+ Before using code patterns, verify installed v...
bio-metagenomics-functional-profiling
Reference examples tested with: HUMAnN 3.8+, MetaPhlAn 4.1+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, se...