القائمة
Skills في هذا المستودع
جمع SkillsMP عدد ٨١٠ من skills من mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-. افتح أي skill لمراجعة مصدره وتفاصيله.
mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-عرض ٤٠ من أصل ٨١٠ skills مجمعة.
Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels. Use when combining multiple plots into publication figures.
لغة النص الأصلي: الإنجليزية
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
لغة النص الأصلي: الإنجليزية
Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use when comparing overlapping gene sets, peak sets, or sample groups with more than 3 sets.
لغة النص الأصلي: الإنجليزية
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib. Use when visualizing differential expression or association results with gene annotations.
لغة النص الأصلي: الإنجليزية
Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering…
لغة النص الأصلي: الإنجليزية
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by…
لغة النص الأصلي: الإنجليزية
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use…
لغة النص الأصلي: الإنجليزية
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating…
لغة النص الأصلي: الإنجليزية
Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules by structural similarity using Butina clustering. Use when finding analogs of a…
لغة النص الأصلي: الإنجليزية
Searches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore features, functional groups, or scaffold matches with atom mapping. Use when finding compounds containing specific chemical moieties or…
لغة النص الأصلي: الإنجليزية
Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking. Prepares receptor PDBQT files, generates ligand conformers, defines binding site boxes, and ranks compounds by predicted binding affinity. Use when screening chemical…
لغة النص الأصلي: الإنجليزية
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
لغة النص الأصلي: الإنجليزية
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
لغة النص الأصلي: الإنجليزية
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.
لغة النص الأصلي: الإنجليزية
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
لغة النص الأصلي: الإنجليزية
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
لغة النص الأصلي: الإنجليزية
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq…
لغة النص الأصلي: الإنجليزية
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream…
لغة النص الأصلي: الإنجليزية
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
لغة النص الأصلي: الإنجليزية
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between…
لغة النص الأصلي: الإنجليزية
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
لغة النص الأصلي: الإنجليزية
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq…
لغة النص الأصلي: الإنجليزية
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use…
لغة النص الأصلي: الإنجليزية
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.
لغة النص الأصلي: الإنجليزية
Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.
لغة النص الأصلي: الإنجليزية
Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling.
لغة النص الأصلي: الإنجليزية
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
لغة النص الأصلي: الإنجليزية
Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads.
لغة النص الأصلي: الإنجليزية
Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.
لغة النص الأصلي: الإنجليزية
Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.
لغة النص الأصلي: الإنجليزية
Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.
لغة النص الأصلي: الإنجليزية
Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immunoprecipitation.
لغة النص الأصلي: الإنجليزية
Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
لغة النص الأصلي: الإنجليزية
Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons.
لغة النص الأصلي: الإنجليزية
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
لغة النص الأصلي: الإنجليزية
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.
لغة النص الأصلي: الإنجليزية
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.
لغة النص الأصلي: الإنجليزية
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR…
لغة النص الأصلي: الإنجليزية
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound…
لغة النص الأصلي: الإنجليزية
Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data. Use when filtering differential expression results, setting significance thresholds, or choosing between correction methods for different study designs.
لغة النص الأصلي: الإنجليزية