Convert BAM files to bigWig and generate genomic heatmaps.
npx skills add https://github.com/hxk622/TokenDance --skill deeptools-hxk622
Please help me install this Agent Skill. Skill: deeptools Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/bioinformatics/deeptools Command: npx skills add https://github.com/hxk622/TokenDance --skill deeptools-hxk622
This Skill simplifies complex Next-Generation Sequencing (NGS) data analysis, enabling researchers to quickly process, visualize, and interpret genomic data from various experiments like ChIP-seq, RNA-seq, and ATAC-seq.
Use the deeptools skill to generate a heatmap of ChIP-seq signal around TSS for your bigWig files and gene annotations.
High-intent search queries and answers about installing and using this skill.
To convert BAM files to bigWig coverage tracks, this Skill processes Next-Generation Sequencing alignment data and generates normalized bigWig files suitable for downstream genomic visualization and sample comparison.
To generate a heatmap of ChIP-seq signal around transcription start sites, this Skill computes a matrix of signal values from bigWig files and gene annotations, producing publication-quality heatmaps and profile plots for clear interpretation.
For NGS data quality control, you can compute sample correlation, perform PCA, and conduct fingerprint analysis to assess the similarity and reliability of your sequencing samples before proceeding with visualization.
Yes, you can analyze ATAC-seq and RNA-seq experiments together, as the Skill supports ChIP-seq, RNA-seq, and ATAC-seq experiments by offering tools for normalization, sample comparison, and genomic feature visualization.
Yes, you need deepTools installed in your environment to run this Skill. It requires deepTools installation and specific input files like BAM, bigWig, and BED/GTF to process and visualize genomic features properly.
Zeyuyang-0420Process genomic interval data and bioinformatics file formats with Polars.
galeepAutomate NGS data processing and analysis with the deepTools suite.
jaechang-hitsProcess and visualize NGS data with deepTools for BAM to bigWig conversion and heatmaps.
jimmc414Convert BAM files to normalized bigWig coverage tracks.
