61 skills · sorted by relevance
Check single-cell RNA-seq data quality, filter low-quality cells using median absolute deviation, a measure of spread, and compare plots before and after filtering. Outputs include filtered data and the original dataset with quality annotations.
Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality, wants to filter for high-quality experiments, needs to interpret quality metrics (FRiP, NSC, RSC, NRF, IDR, TSS enrichment, fragment size), wants to understand ENCODE audit warnings, needs to compare quality across experiments, or is deciding whether data is usable for their analysis. Also use when the user mentions QC, quality control, or data filtering.
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Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64 encodings. Use when analyzing read quality, filtering or trimming low-quality bases, generating quality reports, or deciding which FASTQ quality encoding a file uses before parsing.
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Prepare training datasets for large language models with GPU-assisted cleaning. Covers duplicate removal, quality filtering, and personal information redaction, with workflows for text, images, video, and audio using NeMo Curator.
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
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Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
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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 for downstream analysis.
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Protein design quality control, filtering thresholds, and ranking guidance. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.
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Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.
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Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
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Prepare high-quality datasets for LLM fine-tuning with filtering, deduplication, augmentation, and RLHF data formatting. Activate on: fine-tuning data, training data curation, RLHF dataset, data quality filtering, SFT dataset. NOT for: model training infrastructure (ai-engineer), prompt engineering without fine-tuning (prompt-engineer).
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GPU-accelerated data curation for LLM training. Supports text/image/video/audio. Features fuzzy deduplication (16× faster), quality filtering (30+ heuristics), semantic deduplication, PII redaction, NSFW detection. Scales across GPUs with RAPIDS. Use for preparing high-quality training datasets, cleaning web data, or deduplicating large corpora.
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Prepare high-quality datasets for LLM fine-tuning with filtering, deduplication, augmentation, and RLHF data formatting. Activate on: fine-tuning data, training data curation, RLHF dataset, data quality filtering, SFT dataset. NOT for: model training infrastructure (ai-engineer), prompt engineering without fine-tuning (prompt-engineer).
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GPU-accelerated data curation for LLM training. Supports text/image/video/audio. Features fuzzy deduplication (16× faster), quality filtering (30+ heuristics), semantic deduplication, PII redaction, NSFW detection. Scales across GPUs with RAPIDS. Use for preparing high-quality training datasets, cleaning web data, or deduplicating large corpora.
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Prepare raw credit data for pre-loan modeling by checking data quality and screening variables. Review missing values, predictive usefulness, stability, noise, and correlation, then export an Excel report with organization-level statistics and cleaning results.
Plan or run DNA analysis to find small genetic changes in tumors, using tumor samples alone or paired with normal tissue. Check sample pairing, contamination, data quality, filtering, and annotations that add information to detected variants.
Build or review quality control workflows for single-cell and single-nucleus RNA sequencing data. Select filters from observed data, detect doublets, assign cell types, and create UMAP plots that summarize cell relationships, while recording analysis decisions and outputs.
Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment.
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Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.
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Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.
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Plan or run targeted DNA panel analysis using UMIs, barcodes that identify DNA molecules. Organize consensus reads, coverage checks, and low-frequency variant results with molecular support, filtering reasons, and explicit quality limitations.
Screen US stocks for high-quality dividend opportunities combining value characteristics (P/E ratio under 20, P/B ratio under 2), attractive yields (3% or higher), and consistent growth (dividend/revenue/EPS trending up over 3 years). Supports two-stage screening using FINVIZ Elite API for efficient pre-filtering followed by FMP API for detailed analysis. Use when user requests dividend stock screening, income portfolio ideas, or quality value stocks with strong fundamentals.
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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
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Review code for bugs, logic errors, security vulnerabilities, code quality issues, and adherence to project conventions, using confidence-based filtering to report only high-priority issues that truly matter. Use this skill when reviewing a small set of changes locally (such as unstaged diff), when dispatched as a sub-task during feature-dev quality review, or when the user wants a critique of a specific file or function.
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