deeptools

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

1.50x

Quality

66%

Does it follow best practices?

Impact

90%

1.50x

Average score across 3 eval scenarios

Securityby

Passed

No known issues

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/deeptools/SKILL.md

Evaluation results

92%

44%

RNA-seq Coverage Tracks for Neural Progenitor Transcriptome Study

RNA-seq strand-specific coverage

Criteria

Without context

With context

No --extendReads for RNA-seq

100%

Forward strand filter

100%

Reverse strand filter

100%

CPM normalization

100%

uv install

100%

File validation step

100%

Workflow generator used

20%

Parallel processing

100%

bigWig output format

100%

Commands documented

100%

84%

16%

H3K27ac ChIP-seq Analysis Pipeline for Enhancer Characterization

ChIP-seq analysis workflow

Criteria

Without context

With context

RPGC normalization

100%

Human hg38 genome size

100%

Extend reads for ChIP-seq

100%

Remove duplicates

100%

bamCompare log2 operation

100%

bamCompare readCount scaling

100%

binSize 10

100%

computeMatrix TSS reference-point

100%

Heatmap RdBu colormap

Heatmap kmeans 3

File validation

100%

96%

30%

ATAC-seq Chromatin Accessibility Analysis for Mouse T-cell Activation

ATAC-seq Tn5 offset correction

Criteria

Without context

With context

ATACshift flag

100%

Shifted BAM as coverage input

100%

Fragment size analysis

100%

RPGC normalization

100%

Mouse genome size

66%

100%

bigWig output

100%

File validation step

100%

Workflow generator used

50%

Nucleosome pattern description

66%

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

RNA-seq Coverage Tracks for Neural Progenitor Transcriptome Study H3K27ac ChIP-seq Analysis Pipeline for Enhancer Characterization ATAC-seq Chromatin Accessibility Analysis for Mouse T-cell Activation

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