362 skills · sorted by relevance
Validate FASTQ sequencing files, run local quality checks, and interpret reports to decide whether trimming is needed. Optionally remove adapters or low-quality read ends while preserving original reads and their quality reports.
Get answers about Qwen Code usage, features, configuration, and troubleshooting from its official documentation. The skill also helps inspect and edit user or project settings files when configuration changes are requested.
Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, Trim Galore, featureCounts, Kallisto, Salmon, Picard, GATK logs; merges per-sample stats with plots. For NGS pipeline-wide QC. Use FastQC directly for single-sample; MultiQC for multi-sample reporting.
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Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.
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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.
当用户明确要求"标书QC/质量控制/润色前质检/引用真伪核查/篇幅与结构检查"时使用。对 NSFC 标书进行只读质量控制：并行多线程独立检查文风生硬、引用假引/错引风险、篇幅与章节分布、逻辑清晰度等，最终输出标准化 QC 报告；中间文件默认归档到 `project_root/.bensz-api/task-{yyyymmdd-hhmm}-{简短描述}/nsfc-qc/{yyyy-mm-dd-hh-mm}/`，并兼容 legacy `.nsfc-qc/` 读取/清理。
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Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
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Plan or run bulk RNA-seq processing from sequencing reads to count matrices, tables of expression counts across samples. Check sample metadata, reference consistency, read mapping, and quantification quality, and produce summaries for downstream analysis.
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 preprocessing results.
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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.
Run an initial quality review of public equity investment decks and reports. Identify inconsistent figures, unclear units, missing sources, and conflicting conclusions, then prioritize fixes and document evidence limits in a review report.
Plan or run ATAC-seq analysis to identify accessible DNA regions. Check sequencing quality, align reads, detect peaks, combine evidence across replicate samples, and prepare comparisons between conditions with quality summaries and visualization tracks.
Organize ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag inputs and route them to suitable analysis workflows. Covers initial quality checks and preparation for finding peaks, genomic regions with concentrated signal, and comparing them across samples.
Prepare single-cell or single-nucleus RNA-seq analysis by checking inputs and selecting workflows that turn FASTQ sequencing files into count matrices. Route quality checks, cell annotation, clustering, and UMAP visualization to the embedded downstream skill.
Routes bulk RNA-seq requests to workflows for generating expression counts and checking quality, or comparing gene expression between groups. Checks input data, sample information, and analysis requirements before directing the next step.
Plan or run quality checks and peak calling, which identifies enriched genomic regions, for ChIP-seq, CUT&RUN, and CUT&Tag. The workflow accounts for controls and replicates and prepares signal tracks, quality reports, and differential binding designs.
Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.
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Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers spot and large technical artifacts. Scales linearly with the number of spots and is designed to be used with 'SpatialExperiment' objects.
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cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat
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Apply single-cell rna qc in reproducible local data workflows with version-aware APIs, explicit assumptions, and validation. Use when the user chooses single-cell rna qc or its strengths fit the task.
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제안서 QC 검수 에이전트 (Reviewer) v5.0. proposal_script.md 콘텐츠 품질 + proposal_slides.json 변환 정확성 + proposal.html 시각 품질을 검증합니다. SPARK-6, S-E-P, Win Theme, 패턴 다양성, 분위기 리듬 등 검수. PPTX 모드도 지원. 트리거: QC, 검수, 리뷰, 검증, 체크, 품질, /r
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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.
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Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time alignment, peak-density correspondence, gap-filling, CAMERA redundancy collapse, and built-in QC feature filtering. Use when converting centroided LC-MS runs into a features-by-samples matrix and deciding centWave/grouping/alignment parameters. For drift correction and QC/CV filtering execution see metabolomics/normalization-qc; for metabolite identification see metabolomics/metabolite-annotation; for the MS-DIAL GUI alternative with MS2Dec deconvolution see metabolomics/msdial-preprocessing; for downstream statistics see metabolomics/statistical-analysis.
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Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing values for untargeted LC-MS/GC-MS metabolomics, framing each step as a measurement model that can create or erase biological signal. Use when processing a peak/feature table before statistical analysis, choosing a drift-correction or sample-normalization method, deciding QC RSD vs D-ratio filtering, or handling left-censored missing values. The feature table is produced by metabolomics/xcms-preprocessing or metabolomics/msdial-preprocessing; transformation/scaling for modeling defers to metabolomics/statistical-analysis; cross-study design issues link to experimental-design/batch-design.
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