HolobiomicsLab/asb-skill-collections

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after executing the Juicer pipeline on raw Hi-C FASTQ files, to confirm that the pipeline has generated the expected .hic output artifact and that the contact matrix construction and normalization steps completed without error.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when before running HiC-Pro's normalization stage on aligned Hi-C BAM files. Specifically, when you have SAM/BAM-formatted aligned Hi-C reads that need bias correction and matrix balancing to produce normalized contact maps suitable for downstream chromatin structure analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after generating raw Hi-C contact matrices from aligned reads (post-merge, pre-analysis).

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have completed Hi-C map generation (producing .hic files from aligned reads) and need to detect and annotate topological features such as chromatin loops, topologically associating domains (TADs), or interaction peaks.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a methylBase object containing aligned methylation calls across multiple samples and need to verify whether samples cluster by expected experimental condition (e.g., test vs. control) or identify unexpected sample relationships.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when installing HiC-Pro on a shared HPC cluster or multi-node computing environment where job submission must be routed through a scheduler rather than running locally.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw .idat files or a beta-valued matrix from an Illumina HumanMethylation450 or EPIC array experiment and need to import the full probe set into R for downstream quality control, normalization, and differential methylation analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Illumina EPIC or 450k methylation array data (.idat files or beta-valued matrices) and need to perform comprehensive quality assessment, probe correction, batch effect adjustment, and identification of differentially methylated regions or blocks across sample groups.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when your input is raw .idat files or a beta-valued matrix from Illumina HumanMethylation450 or EPIC arrays, and you need to remove unreliable probes (those with detection p-value > 0.01 or insufficient bead counts) before performing differential methylation or other downstream analyses.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after running ChAMP detection functions (champ.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when you have aligned paired scATAC-seq and scRNA-seq data from the same cells (multiome data) and need to create a single reduced-dimension coordinate space that integrates both chromatin accessibility and gene expression signals for joint clustering, trajectory analysis, or visualization.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating domains, or annotate other structural features without re-running the full alignment and contact matrix construction.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Hi-C FASTQ files from a high-throughput chromatin conformation capture experiment and need to generate a normalized contact matrix (.hic file) for downstream genomic analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have paired-end Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited) and need to produce standardized .hic binary contact maps that conform to ENCODE reference formats and integrity standards for downstream 3D genome analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have raw Hi-C FASTQ data and need to generate contact maps at kilobase resolution, or you have pre-generated .hic files and need to annotate structural features (loops, domains) for downstream 3D genome analysis.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have filtered peak counts from ATAC or DNase-seq data (with GC bias correction and sample/peak filtering applied) and want to annotate peaks by k-mer content rather than known transcription factor motifs—particularly when comparing how k-mer size affects the magnitude of chromatin.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when after computing deviations for both motif and kmer annotations on the same chromVAR dataset, when you need to determine whether kmers and motifs are redundant predictors of chromatin accessibility variability or provide complementary information for downstream clustering, annotation, or.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have a single-cell count matrix with 10 million or more cells that must be processed through dimension reduction, clustering, or integration pipelines. Use it specifically before executing matrix-free spectral embedding (tl.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have performed spectral dimension reduction on single-cell omics count matrices and wish to partition cells into discrete populations.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you are building or extending a multi-module Python library for scientific computation (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when you have paired ChIP and control BED/BEDPE files and need to account for local sequencing bias before peak calling. Use it specifically when control signal varies across genomic regions at multiple spatial scales (e.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when performing ChIP-Seq peak calling with MACS3, after duplicate filtering and fragment length prediction (d), to construct the background model that will be compared against ChIP signal.

HolobiomicsLab/asb-skill-collections

Skill Claude CodeCodex

Use when when you have aligned ChIP-Seq reads (BED or BEDPE format) and a corresponding control sample, and you need explicit control over peak-calling parameters—including fragment-length prediction, local bias windows (d, slocal=1kb, llocal=10kb), background scaling, and score-cutoff.