HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when you have executed an end-to-end SnapATAC2 pipeline on the pbmc10kmultiome dataset (or a similar single-cell ATAC-seq dataset with a published reference) and need to validate that spectral embedding, Leiden clustering, and UMAP layout have converged to expected cluster identities and.
HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when when you need to reproduce or validate benchmark comparisons between clustering methods on single-cell chromatin accessibility data, particularly when the source publication reports multiple accuracy metrics across heterogeneous datasets and you must decide which method variant (e.
HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when when you have a binned Hi-C cooler file, an associated eigenvector track (from prior eigscis calculation), and need to measure how strongly the genome is partitioned into active (A) and inactive (B) compartments.
HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when you have a raw or preprocessed single-cell count matrix (from BAM-to-fragment or FASTQ-to-matrix pipelines) and need to apply matrix-free algorithms like tl.spectral, tl.multispectral, or other scalable dimension reduction methods that require dense or sparse matrix input.
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.