HolobiomicsLab/asb-skill-collections

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when analyzing differential methylation from bisulfite sequencing data where you suspect overdispersion (variance exceeds binomial expectations), or when comparing uncorrected and corrected statistical tests to determine whether more stringent thresholds are justified by the data.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragmentpaired'] or .

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have run a peak-calling algorithm on sparse CUT&RUN bedGraph data and received a BED-format output file.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after clustering single-cell ATAC-seq data (e.g., via Leiden clustering on spectral embeddings), use this skill to identify peaks within each cluster. Triggering conditions: (1) you have sparse, per-cell insertion counts organized in a tile matrix.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when developing or reviewing Python code for a scientific package (e.g., cooltools) that targets collaborative development with multiple contributors.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after extending ChIP sample reads to their predicted fragment length and constructing local lambda bias tracks (incorporating d-scaled, 1 kb, 10 kb, and genome-wide backgrounds).

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after generating ChIP pileup and local lambda (background) BEDGRAPH tracks with matched sequencing depth, use this skill to assign statistical significance scores to each genomic region.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have ATAC-seq BAM alignments with classified motif sites (bound vs. unbound based on chromatin accessibility or binding thresholds) and wish to detect and visualize the characteristic Tn5 insertion depletion signal (footprints) around transcription factor binding sites.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after merging methylation call files from multiple samples using unite() to create a methylBase object, apply PCA when you need to visualize sample-level relationships based on overall methylation similarity across all covered bases, or when you want to determine which principal components.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when immediately after loading raw methylation array data (.idat files or beta-valued matrix) from HumanMethylation450 (450k) or EPIC arrays when conducting primary quality control.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after implementing or modifying Python library functions (such as utility functions in cooltools.lib subpackages) to verify correctness and identify gaps in test coverage before merging changes or releasing code.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when setting up a new conda environment for a Python-based bioinformatics pipeline and you need to confirm that all declared dependencies (e.g., pysam >=0.15.4, bx-python >=0.8.8, numpy >=1.18.1, scipy >=1.4.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you are preparing to run Hi-C data normalization or read alignment filtering steps that depend on Python modules (iced, pysam, numpy, scipy) and you need to ensure consistent module versions across multiple runs or compute nodes.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you are building or refactoring a scientific Python library and need to decide how to organize and expose utility functions (e.g., adaptive coarse-graining, filtering, analysis routines) so that end users can import and call them reliably.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have precomputed expected contact frequency tables (TSV format with columns like distbp, contactfrequency, nvalid) and need to apply log-binning and smoothing to group distance values into log-spaced bins, aggregate statistics within each bin, and export a cleaned, annotated output.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when you have raw methylation array data (450K or EPIC format) in .idat files or as a beta-valued matrix and need to conduct a complete analysis pipeline including data import, quality filtering, normalization, batch effect correction, DMR detection, or gene set enrichment.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after installing R or modifying an R environment via conda, package managers, or container images; before running any pipeline step that depends on R packages for statistical analysis, visualization, or data normalization.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when analyzing normalized DNA methylation beta matrices (450K or EPIC arrays) and you need to identify the true number of latent batch or technical factors present in the data.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have identified a published computational tool (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin accessibility and gene expression signals.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a cooler Hi-C contact matrix file and an associated eigenvector track (from prior eigscis calculation or similar), and you need to quantify the preferential interaction patterns between A and B chromatin compartments.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after merging methylation calls across all samples using unite() to create a methylBase object, apply this skill to characterize whether replicate samples cluster together and to visualize methylation-driven separation between biological groups (e.g., test vs. control).

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after completing peak calling and cell annotation in an ArchR project, when you intend to perform trajectory analysis using STREAM rather than ArchR's native monocle3 or Slingshot integrations, or when you need to share peak-by-cell matrices with collaborators using STREAM pipelines.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when use this skill during pipeline installation or initialization when you need to locate required external binaries (e.g., bowtie2, samtools, R, Python) but the user has not explicitly provided their installation paths in a configuration file.