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SkillsMP has collected 810 skills from mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-. Open a skill to review its source and details.
mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-Showing 40 of 810 collected skills.
Analyzes time-to-event data using Kaplan-Meier curves, log-rank tests, and Cox proportional hazards regression with lifelines. Builds survival models from clinical and omics features. Use when predicting patient survival or modeling time-to-event outcomes.
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classes, chain composition, or lipid-specific pathways.
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before statistical analysis.
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when identifying differentially abundant metabolites or building classification models.
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves and internal standards.
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for…
Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome…
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis. Use when performing supervised multi-omics integration or identifying features that discriminate…
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving…
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity…
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone…
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic,…
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have poor quality tails or require minimum quality…
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating…
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. Use when validating RNA-seq libraries before differential expression analysis.
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to…
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma…
Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor…
Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns…
Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or…
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for…
Estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations via HMM segmentation and calculates ctDNA percentage. Requires 0.1-1x sWGS coverage. Use when quantifying tumor burden from liquid…
Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein…
Detect horizontal gene transfer events using HGTector, compositional analysis, and phylogenetic incongruence methods. Identify foreign genes in bacterial and archaeal genomes from anomalous composition or unexpected phylogenetic placement. Use when searching…
Infer orthologous gene groups across species using OrthoFinder and ProteinOrtho. Identify orthologs, paralogs, and co-orthologs for comparative genomics and functional annotation transfer. Use when identifying gene orthologs across species or building…
Detect positive selection using dN/dS (omega) tests with PAML codeml and HyPhy. Identify sites and branches under adaptive evolution through codon models and branch-site tests. Use when testing for adaptive evolution in gene families or identifying positively…