mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- - 20ページ

bio-small-rna-seq-mirdeep2-analysis

Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data. Use when identifying new miRNAs or performing comprehensive miRNA profiling with discovery.

原文の言語: 英語

bio-small-rna-seq-mirge3-analysis

Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA editing.

原文の言語: 英語

bio-small-rna-seq-smrna-preprocessing

Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.

原文の言語: 英語

bio-small-rna-seq-target-prediction

Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally important miRNAs.

原文の言語: 英語

bio-workflow-management-cwl-workflows

Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing…

原文の言語: 英語

bio-workflow-management-nextflow-pipelines

Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with container support, running workflows on cloud platforms (AWS, Google Cloud), or…

原文の言語: 英語

bio-workflow-management-snakemake-workflows

Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution. Use when creating Python-based workflows, automating multi-step analyses with make-like dependency tracking, or running pipelines on HPC…

原文の言語: 英語

bio-workflow-management-wdl-workflows

Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GATK best practices pipelines, working with Terra/AnVIL platforms, or building workflows for cloud execution on…

原文の言語: 英語

bio-workflows-atacseq-pipeline

End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting. Use when running end-to-end ATAC-seq analysis from FASTQ to differential…

原文の言語: 英語

bio-workflows-biomarker-pipeline

End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV, and SHAP interpretation. Use when building and validating diagnostic or prognostic…

原文の言語: 英語

bio-workflows-chipseq-pipeline

End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.

原文の言語: 英語

bio-workflows-clip-pipeline

End-to-end CLIP-seq analysis from FASTQ to binding sites and motif enrichment. Use when analyzing protein-RNA interactions from CLIP-based methods.

原文の言語: 英語

bio-workflows-cnv-pipeline

End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.

原文の言語: 英語

bio-workflows-crispr-editing-pipeline

End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR…

原文の言語: 英語

bio-workflows-crispr-screen-pipeline

End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods. Use when analyzing pooled CRISPR screens from count data to hit calling.

原文の言語: 英語

bio-workflows-cytometry-pipeline

End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.

原文の言語: 英語

bio-workflows-expression-to-pathways

Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.

原文の言語: 英語

bio-workflows-fastq-to-variants

End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.

原文の言語: 英語

bio-workflows-genome-assembly-pipeline

End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches. Use when assembling genomes from raw reads.

原文の言語: 英語

bio-workflows-gwas-pipeline

End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative traits. Use when running genome-wide association studies.

原文の言語: 英語

bio-workflows-hic-pipeline

End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization. Use when processing Hi-C data to compartments and TADs.

原文の言語: 英語

bio-workflows-imc-pipeline

End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statistics. Use when analyzing imaging mass cytometry data end-to-end.

原文の言語: 英語

bio-liquid-biopsy-pipeline

Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy…

原文の言語: 英語

bio-workflows-longread-sv-pipeline

End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.

原文の言語: 英語

bio-workflows-merip-pipeline

End-to-end MeRIP-seq analysis from FASTQ to m6A peaks and differential methylation. Use when analyzing epitranscriptomic m6A modifications from immunoprecipitation data.

原文の言語: 英語

bio-workflows-metabolic-modeling-pipeline

End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA analysis, and gene essentiality prediction. Use when building metabolic models or…

原文の言語: 英語

bio-workflows-metabolomics-pipeline

End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping. Use when processing LC-MS metabolomics data.

原文の言語: 英語

bio-workflows-metagenomics-pipeline

End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.

原文の言語: 英語

bio-workflows-methylation-pipeline

End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.

原文の言語: 英語

bio-workflows-microbiome-pipeline

End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.

原文の言語: 英語

bio-workflows-multi-omics-pipeline

End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics…

原文の言語: 英語

bio-workflows-multiome-pipeline

End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.

原文の言語: 英語

bio-workflows-neoantigen-pipeline

End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immunogenicity scoring. Use when identifying tumor neoantigens for personalized vaccine design…

原文の言語: 英語

bio-workflows-outbreak-pipeline

End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen…

原文の言語: 英語

bio-workflows-proteomics-pipeline

End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma. Use when processing mass spectrometry proteomics.

原文の言語: 英語

bio-workflows-riboseq-pipeline

End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.

原文の言語: 英語

bio-workflows-rnaseq-to-de

End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization. Use when running RNA-seq from FASTQ to DE results.

原文の言語: 英語

bio-workflows-scrnaseq-pipeline

End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.

原文の言語: 英語

bio-workflows-smrna-pipeline

End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.

原文の言語: 英語

bio-workflows-somatic-variant-pipeline

End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer genomics. Use when calling somatic mutations from tumor-normal pairs.

原文の言語: 英語