HolobiomicsLab/asb-skill-collections

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when an algorithm claims linear or sublinear time/space complexity (e.g., matrix-free spectral embedding) and you need to verify that claim holds for datasets at the scale intended (10 million+ cells).

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you need to deploy a complex multi-language pipeline (e.g., HiC-Pro) that requires Python >3.7 libraries (pysam, bx-python, numpy, scipy), R packages (ggplot2, RColorBrewer), and compiled tool binaries (bowtie2, samtools >=1.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when deploying a complex bioinformatics pipeline (like HiC-Pro) across heterogeneous computing environments where required tools (bowtie2, samtools, R, Python) may be installed in non-standard locations, differ in version, or require scheduler-specific configuration (TORQUE, SGE, SLURM.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a precomputed expected contact frequency table (TSV format with columns: distbp, contactfrequency, nvalid) derived from cooler files and need to compress distance-dependent contact probabilities into log-spaced bins.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a cooler Hi-C contact matrix, a set of genomic features (e.g., CTCF peaks, enhancers, or TAD boundaries defined in BED format), and want to quantify average contact patterns around those features to detect local organization principles.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a precomputed expected contact frequency table (TSV with columns: distbp, contactfrequency, nvalid) derived from cooler Hi-C matrices and need to generate a smoothed, log-binned P(s) curve for downstream analysis such as TAD detection, contact probability visualization, or.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a Hi-C dataset stored in cooler format (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when your Hi-C data is stored in cooler format (a binary HDF5-based sparse matrix with associated genomic bins and genomic tracks); you need to programmatically access the contact matrix, bin coordinates, or track data (e.g., eigenvectors, GC content) for further analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you are performing dimensionality reduction on a sparse single-cell count matrix (in CSR format) and need to compute pairwise cell similarities before spectral decomposition.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after calculateDiffMeth() has been run on a methylBase object and you have a methylDiff object with q-values and methylation difference estimates.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a methylDiff object containing differentially methylated bases or regions from bisulfite sequencing, gene annotation in BED or similar format (RefSeq, Ensembl), and CpG island coordinate files, and need to understand what fraction of your differential methylation signal falls.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have paired scATAC-seq peak matrices and scRNA-seq gene expression matrices from the same cells (multiome data) and need to perform joint clustering, visualization, or correlation analysis across both chromatin accessibility and gene expression in a single coordinate system.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when setting up HiC-Pro or similar multi-tool pipelines where tool availability and version constraints are prerequisites for downstream analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when before running HiC-Pro or similar multi-stage pipelines on a new system or environment, especially when dependency installation is not automated (e.g., not in a conda environment or container).

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have filtered ATAC-seq peak counts, matched motifs to those peaks, and want to measure which transcription factor motifs show elevated or reduced accessibility relative to GC-content and accessibility-matched background expectations—particularly when annotating TF motif usage across.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after identifying differentially accessible peaks (via tl.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have pre-processed chromatin accessibility data (ATAC-seq or DNAse-seq) with chromVAR deviations already computed for individual cells or bulk samples across multiple cell types or conditions, and you need to identify which transcription factor motifs exhibit significant differential.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have aligned ATAC-seq BAM files and peak annotations from two or more experimental conditions (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have preprocessed, normalized beta-value matrices from EPIC or 450k methylation arrays with at least two sample groups (case/control, treatment/untreated, or similar contrasts) and seek to identify regions of coordinated differential methylation rather than individual CpG sites.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw .idat files or beta-valued matrices from Illumina HumanMethylation450 (450K) or EPIC array experiments and need to import them into R for quality control and downstream analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have loaded normalized methylation data from EPIC or 450k arrays and need to identify differentially methylated blocks rather than individual CpG sites or DMRs.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have merged methylation call data across multiple biological replicates (samples per group ≥2) with base-pair-level coverage information, and you need to identify loci where methylation levels differ significantly between treatment groups.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have CpG methylation call files (from Bismark or MethylDackel) and need to load them into R for differential methylation analysis, but anticipate memory constraints or want to avoid loading the entire dataset into memory.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when immediately after loading raw .idat files or beta-value matrices from HumanMethylation450 or EPIC arrays when you need to exclude probes that fail quality control.