mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- - 19ページ

bio-sequence-properties

Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.

原文の言語: 英語

bio-sequence-slicing

Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.

原文の言語: 英語

bio-transcription-translation

Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.

原文の言語: 英語

bio-structural-biology-alphafold-predictions

Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

原文の言語: 英語

bio-pdb-geometric-analysis

Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).

原文の言語: 英語

bio-structural-biology-modern-structure-prediction

Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel proteins, protein complexes, or when comparing predictions across multiple methods.

原文の言語: 英語

bio-pdb-structure-io

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

原文の言語: 英語

bio-pdb-structure-modification

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

原文の言語: 英語

bio-pdb-structure-navigation

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

原文の言語: 英語

bio-systems-biology-context-specific-models

Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating…

原文の言語: 英語

bio-systems-biology-flux-balance-analysis

Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy. Predict growth rates, metabolic fluxes, and optimal resource utilization. Use when predicting metabolic phenotypes or optimizing flux…

原文の言語: 英語

bio-systems-biology-gene-essentiality

Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding…

原文の言語: 英語

bio-systems-biology-metabolic-reconstruction

Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis. Use when creating metabolic models for organisms without existing models.

原文の言語: 英語

bio-systems-biology-model-curation

Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing…

原文の言語: 英語

bio-differential-splicing

Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment…

原文の言語: 英語

bio-isoform-switching

Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions. Use when investigating how splicing changes affect…

原文の言語: 英語

bio-sashimi-plots

Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes differential splicing events with grouped samples and junction read support. Use when visualizing specific splicing events or…

原文の言語: 英語

bio-single-cell-splicing

Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. Identifies cell-type-specific splicing patterns. Use when analyzing isoform usage in scRNA-seq…

原文の言語: 英語

bio-splicing-qc

Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC. Use when evaluating data suitability for splicing analysis or troubleshooting low event…

原文の言語: 英語

bio-splicing-quantification

Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files. Calculates inclusion levels for skipped exons, alternative splice sites, mutually exclusive exons, and retained…

原文の言語: 英語

bio-differential-expression-batch-correction

Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.

原文の言語: 英語

bio-de-results

Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when…

原文の言語: 英語

bio-de-visualization

Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.

原文の言語: 英語

bio-de-deseq2-basics

Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis…

原文の言語: 英語

bio-de-edger-basics

Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when…

原文の言語: 英語

bio-differential-expression-timeseries-de

Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when analyzing time-series or longitudinal expression data.

原文の言語: 英語

bio-expression-matrix-counts-ingest

Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.

原文の言語: 英語

bio-expression-matrix-gene-id-mapping

Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.

原文の言語: 英語

bio-expression-matrix-metadata-joins

Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.

原文の言語: 英語

bio-expression-matrix-sparse-handling

Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.

原文の言語: 英語

bio-ribo-seq-orf-detection

Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated regions beyond annotated coding sequences or quantifying ORF-level translation.

原文の言語: 英語

bio-ribo-seq-riboseq-preprocessing

Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.

原文の言語: 英語

bio-ribo-seq-ribosome-periodicity

Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determining read offsets for downstream analysis.

原文の言語: 英語

bio-ribo-seq-ribosome-stalling

Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon-specific translation dynamics.

原文の言語: 英語

bio-ribo-seq-translation-efficiency

Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.

原文の言語: 英語

bio-rna-quantification-alignment-free-quant

Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.

原文の言語: 英語

bio-rna-quantification-count-matrix-qc

Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.

原文の言語: 英語

bio-rna-quantification-featurecounts-counting

Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.

原文の言語: 英語

bio-rna-quantification-tximport-workflow

Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.

原文の言語: 英語

bio-small-rna-seq-differential-mirna

Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.

原文の言語: 英語