holobiomicslab/asb-skill-collections
58 skills
$npx skills add holobiomicslab/asb-skill-collectionsSkillInstalls
450k-array-data-processingUse when you have raw .idat files or beta-valued matrices from HumanMethylation450 (450k) arrays and need to remove low-quality probes, correct for technical…anndata-backed-object-manipulationUse when when working with large single-cell ATAC-seq or multi-omics datasets where in-memory storage is infeasible (>1M cells), and you need to iteratively…archr-project-manipulationUse when you have a processed ArchR project object (containing peak calls, cell barcodes, and quality control metadata) and need to: (1) reduce dimensionality…atac-seq-bam-read-alignment-processingUse when when you have aligned ATAC-seq BAM files and need to quantify Tn5 transposase insertion patterns around specific genomic coordinates (motif sites,…atac-seq-clustering-performance-interpretationUse when when you need to assess whether a given ATAC-seq clustering method (or variant) is competitive on your data or when evaluating which published method…atac-seq-feature-matrix-constructionUse when when you have processed scATAC-seq data (peak calling complete, cell-barcode matrix generated) and need to register it into ArchR for downstream…atac-seq-footprint-scoringUse when you have completed Tn5 insertion bias correction on ATAC-seq reads and now need to quantify footprint signal strength (signal depletion around…atac-seq-peak-annotationUse when after differential peak analysis (tl.diff_test) has identified peaks that differ in accessibility across cell types or conditions.atac-seq-signal-normalizationUse when you have aligned ATAC-seq BAM files and need to detect transcription factor binding sites via footprint analysis.atac-seq-tn5-bias-correctionUse when you have raw ATAC-seq BAM files and need to perform footprinting analysis to detect transcription factor binding through Tn5 insertion patterns.background-peak-selection-normalizationUse when after computing expected accessibility from filtered peak and sample counts, and before computing final deviation scores.bam-file-coordinate-sorting-verificationUse when before invoking pp.make_fragment_file on a BAM file from alignment or external sources, especially when the BAM's sort order is unknown or when…bam-to-bigwig-conversionUse when after running TOBIAS ATACorrect to generate bias-corrected signal tracks from aligned ATAC-seq reads.bam-to-fragment-file-conversionUse when when you have coordinate-sorted BAM files from single-cell ATAC-seq experiments (e.g., 10X Genomics scATAC-seq) and need to generate a compressed…barcode-fragment-mappingUse when you have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment…bead-count-threshold-filteringUse when apply this filter after loading raw .idat files or beta-valued matrices from HumanMethylation450 or EPIC methylation arrays when you need to remove…bed-format-generation-from-dataframeUse when you have extracted quantitative genomic features (e.g., insulation scores, boundary annotations) as a pandas DataFrame with bin coordinates and…bedgraph-file-exportUse when after computing per-bin coverage depth using cooltools.coverage() on a loaded cooler object, when you need to (1) share the coverage track with…bedgraph-file-format-manipulationUse when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or…bedgraph-format-parsing-and-validationUse when you have generated or received bedGraph files from paired-end sequencing (via bedtools genomecov or similar) and need to verify they conform to UCSC…bedpe-format-handlingUse when your ChIP-Seq input is paired-end sequencing data stored in BEDPE format (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.gz), and you need to estimate fragment…benchmark-table-parsing-and-aggregationUse when you are reproducing a comparative benchmarking claim (e.bias-corrected-z-score-interpretationUse when after computeDeviations has generated a SummarizedExperiment object with z-score assays reflecting bias-corrected deviations of observed vs.bigwig-signal-processingUse when after bias correction of ATAC-seq reads (via ATACorrect) when you have a bias-corrected bigWig file and need to measure transcription factor footprint…bin-level-sequencing-depth-calculationUse when you have a cooler file (.cool or .mcool) from a Hi-C or micro-C experiment and need to quantify the total number of sequencing reads assigned to each…binary-path-detection-and-validationUse when when setting up a bioinformatics pipeline (particularly Hi-C data processing) that depends on multiple external binaries with version constraints, and…bioinformatics-tool-binary-path-resolutionUse when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to…bioinformatics-tool-version-compatibility-assessmentUse when before executing a complex bioinformatics pipeline (such as Hi-C data processing) that depends on multiple third-party tools with explicit version…bisulfite-sequencing-data-loadingUse when you have raw methylation call files from Bismark, MethylDackel, or similar bisulfite alignment tools (bedGraph, cytosine report, or tabix-indexed…bootstrap-confidence-interval-computationUse when when you have computed z-score deviations for genomic annotations (e.g., motifs) across multiple cells or samples and need to quantify uncertainty in…boundary-detection-thresholdingUse when when you have computed per-bin insulation scores from a Hi-C cooler file using cooltools.insulation and need to identify discrete genomic boundaries…checksum-verification-for-reproducibilityUse when you have executed a complex multi-step processing pipeline (e.g., ENCODE Hi-C uniform processing pipeline) and need to confirm that the generated…chip-seq-peak-calling-workflowUse when when you have aligned ChIP-Seq reads (single-end BED or paired-end BEDPE format) and need to identify enriched genomic regions by comparing ChIP…chip-seq-read-alignment-filteringUse when when beginning peak calling on ChIP-Seq data: you have raw single-end or paired-end BED/BEDPE alignment files for both ChIP and control samples and…chip-seq-signal-pileup-extensionUse when after duplicate filtering and fragment length prediction (d) in ChIP-Seq analysis, when you need to convert discrete read alignments into continuous…chromatin-accessibility-bias-correctionUse when you have loaded raw ATAC-seq fragment counts into a SummarizedExperiment object and are preparing to compute motif deviations.chromatin-accessibility-binding-status-classificationUse when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which…chromatin-accessibility-deviation-computationUse when when you have filtered ATAC-seq or DNAse-seq peak counts (after GC bias correction, sample filtering, and peak filtering) and wish to measure how…chromatin-accessibility-footprint-visualizationUse when use this skill after performing Tn5 bias correction and footprint scoring on ATAC-seq BAM files when you need to inspect the spatial distribution of…chromatin-accessibility-occupancy-predictionchromatin-accessibility-quantificationchromatin-accessibility-variability-rankingUse when you have sparse, single-cell or bulk ATAC/DNAse-seq data from multiple cell types or conditions (e.g., GM vs H1 cell lines), pre-filtered and…chromatin-domain-boundary-detectionUse when you have generated a .hic contact map from Hi-C raw sequencing data and need to identify topologically associating domains (TADs) or other chromatin…cis-contact-frequency-analysisUse when when you have loaded a cooler file containing Hi-C contact matrices and need to quantify how contact probability decays with genomic distance within a…cluster-umap-layout-reproducibility-benchmarkingUse when you have executed an end-to-end SnapATAC2 pipeline on the pbmc10k_multiome dataset (or a similar single-cell ATAC-seq dataset with a published…clustering-accuracy-metric-extractionUse when when you need to reproduce or validate benchmark comparisons between clustering methods on single-cell chromatin accessibility data, particularly when…compartment-strength-quantificationUse when when you have a binned Hi-C cooler file, an associated eigenvector track (from prior eigs_cis calculation), and need to measure how strongly the…compressed-sparse-row-matrix-handlingUse 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…computational-complexity-validationUse 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…conda-environment-creation-and-managementUse 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…configuration-file-generation-and-templatingUse when when deploying a complex bioinformatics pipeline (like HiC-Pro) across heterogeneous computing environments where required tools (bowtie2, samtools,…contact-distance-binning-logarithmicUse when you have a precomputed expected contact frequency table (TSV format with columns: dist_bp, contact_frequency, n_valid) derived from cooler files and…contact-frequency-aggregation-by-genomic-featureUse 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…contact-frequency-smoothing-log-spaceUse when you have a precomputed expected contact frequency table (TSV with columns: dist_bp, contact_frequency, n_valid) derived from cooler Hi-C matrices and…cooler-file-format-handlingcooler-file-loading-and-queryingUse 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…cosine-similarity-metric-applicationUse when you are performing dimensionality reduction on a sparse single-cell count matrix (in CSR format) and need to compute pairwise cell similarities before…cpg-base-filtering-by-statistical-thresholdUse when after calculateDiffMeth() has been run on a methylBase object and you have a methylDiff object with q-values and methylation difference estimates.