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bio-metabolomics-targeted-analysis
Reference examples tested with: ggplot2 3.5+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scikit-learn 1.4+, scipy 1.12+, xcms 4.0+ Before using code p...
bio-metabolomics-xcms-preprocessing
Reference examples tested with: MSnbase 2.28+, scanpy 1.10+, xcms 4.0+ Before using code patterns, verify installed versions match. If versions differ...
bio-metagenomics-abundance
Reference examples tested with: Bracken 2.9+, Kraken2 2.1+, MetaPhlAn 4.1+, pandas 2.2+ Before using code patterns, verify installed versions match. I...
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+, seaborn 0.13+ Before using code ...
bio-metagenomics-kraken
Reference examples tested with: Kraken2 2.1+, MetaPhlAn 4.1+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions dif...
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 code patterns, verify installed...
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+ Before using code patterns, veri...
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+, scikit-learn 1.4+, scipy 1.1...
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+ Before using code patterns, verif...
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 patterns, verify installed versio...
bio-methylation-calling
Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <package...
bio-methylation-dmr-detection
Reference examples tested with: GenomicRanges 1.54+ Before using code patterns, verify installed versions match. If versions differ: R: packageVersion...