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Data analysis, BI, visualization, datasets, statistics, and ML workflows
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Showing 1,369–1,392 of 12,625 skills
- Bio Metabolomics Statistical AnalysisStatistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when identifying differentially abundant metabolites or building classification models.Votes: 0GitHub stars: 2
- Bio Metabolomics LipidomicsSpecialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classes, chain composition, or lipid-specific pathways.Votes: 0GitHub stars: 2
- Bio Longread AlignmentAlign long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.Votes: 0GitHub stars: 2
- Bio Imaging Mass Cytometry Spatial AnalysisSpatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for neighborhood enrichment, or identifying cell-cell interaction patterns in imaging mass cytometry data.Votes: 0GitHub stars: 2
- Bio Imaging Mass Cytometry Quality MetricsQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.Votes: 0GitHub stars: 2
- Bio Imaging Mass Cytometry PhenotypingCell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.Votes: 0GitHub stars: 2
- Bio Imaging Mass Cytometry Interactive AnnotationInteractive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.Votes: 0GitHub stars: 2
- Bio Imaging Mass Cytometry Data PreprocessingLoad and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.Votes: 0GitHub stars: 2
- Bio Imaging Mass Cytometry Cell SegmentationCell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Tad DetectionCall topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Matrix OperationsBalance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Loop CallingDetect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Hic VisualizationVisualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Hic DifferentialCompare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Hic Data IoLoad, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Contact PairsProcess Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.Votes: 0GitHub stars: 2
- Bio Hi C Analysis Compartment AnalysisDetect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.Votes: 0GitHub stars: 2
- Bio Genome Intervals Interval ArithmeticCore interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent intervals, or transferring annotations between interval files.Votes: 0GitHub stars: 2
- Bio Genome Intervals Coverage AnalysisCalculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.Votes: 0GitHub stars: 2
- Bio Gatk Variant CallingVariant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.Votes: 0GitHub stars: 2
- Bio Flow Cytometry Gating AnalysisManual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strategies.Votes: 0GitHub stars: 2
- Bio Flow Cytometry Fcs HandlingRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.Votes: 0GitHub stars: 2
- Bio Flow Cytometry Doublet DetectionDetect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis.Votes: 0GitHub stars: 2
- Bio Flow Cytometry Differential AnalysisDifferential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.Votes: 0GitHub stars: 2