HolobiomicsLab/asb-skill-collections

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages, Python libraries) and you need to verify their availability and configure their paths before running the analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when benchmarking or validating the scalability of single-cell algorithms that claim linear or sublinear space complexity, particularly when processing datasets with ≥10 million cells.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have extracted clustering or classification accuracy metrics (NMI, ARI, purity scores) for two or more competing methods evaluated on multiple datasets, and need to determine which method performs overall rather than on individual datasets alone.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have loaded a normalized beta-valued methylation matrix (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after merging methylation call files across all samples into a unified methylBase object (via unite()), when you need to assess whether biological replicates cluster together, identify unexpected sample groupings, or visualize global methylation similarity relationships before proceeding.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after calculating differential methylation across samples using calculateDiffMeth(), when you need to separately enumerate and extract hyper-methylated (increased methylation) versus hypo-methylated (decreased methylation) bases that meet both statistical significance (q-value < 0.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have loaded individual methylation call files as methylRawList objects from bisulfite sequencing experiments (via methRead()) and need to perform base-level comparative analysis across two or more samples.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when immediately after loading raw methylation array data using champ.load() or champ.import() to verify data integrity.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after identifying differentially methylated bases or regions (via calculateDiffMeth() and getMethylDiff()), when you need to characterize WHERE these methylation changes occur relative to gene structure and CpG density landscapes.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have loaded normalized methylation beta-value matrices from Illumina EPIC or 450k arrays and need to move beyond single-CpG differential methylation testing to identify multi-CpG regions with coordinated differential methylation signals.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after reading in per-sample methylation call files with methRead() and obtaining methylRawList objects, but before calculating differential methylation or performing annotation.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when analyzing DNA methylation data from bisulfite sequencing (RRBS, target-capture, or whole-genome) and the dataset is too large to fit comfortably in memory, or when you need to process multiple large samples sequentially without reloading data.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when before invoking any Python module in a multi-step Hi-C processing pipeline, or when a dependency has been freshly installed or reinstalled.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have an ArchR project object with dimensionality reduction results (LSI or combined dimensions from scATAC-seq ± scRNA-seq) and want to infer pseudotime trajectories and cell-state transitions.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a chromVARDeviations object with multiple annotation sets (such as JASPAR motifs and kmers) and need to determine which annotation pairs are redundant (high correlation) versus synergistic (high synergy z-scores).

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after identifying a set of differentially accessible peaks (via tl.difftest or equivalent), when you need to infer which transcription factors may regulate the observed chromatin state changes.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a filtered set of non-overlapping peaks from ATAC-seq data and a collection of motifs (typically from JASPAR or similar databases), and you need to identify which peaks contain matches to which motifs as a prerequisite for computing motif-based deviation scores across samples.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have bias-corrected ATAC-seq footprint signals (BigWig files) from two or more distinct conditions (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have independently generated or received both scATAC-seq peak count matrices and scRNA-seq gene expression matrices from the same set of cells (multiome experiment), and you need to perform joint analysis such as co-clustering, trajectory inference, or regulatory inference that.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after generating a q-value bedgraph track from ChIP-Seq pileup versus local lambda comparison, and you need to identify statistically significant narrow peaks with defined boundaries.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after running macs3 callpeak with the -f BEDPE flag on paired-end ChIP-Seq data (e.g., CTCFPEChIPchr2250k.bedpe.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have aligned ATAC-seq BAM files and want to discriminate between transcription factor binding sites that are actually occupied by protein versus sites with matching sequence motifs that are unbound.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after applying a quantitative analysis function (e.g., cooltools.insulation, contact frequency calculations) to Hi-C cooler files or other genomic datasets, validate that the output numeric columns contain values within plausible ranges (e.