All categories
Data & Analytics
Data analysis, BI, visualization, datasets, statistics, and ML workflows
- 13,012
- 543
Security grades appear on each card once the skill has been scanned. Newly imported skills may briefly show without a grade until the backfill job runs.
Open in full browserBrowse data & analytics skills
Showing 1,873–1,896 of 13,012 skills
- 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
- Bio Flow Cytometry Cytometry QcComprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.Votes: 0GitHub stars: 2
- Bio Flow Cytometry Compensation TransformationSpillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.Votes: 0GitHub stars: 2
- Bio Flow Cytometry Bead NormalizationBead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.Votes: 0GitHub stars: 2
- Bio Expression Matrix Gene Id MappingConvert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when you need to map IDs for pathway analysis or to match different data sources.Votes: 0GitHub stars: 2
- Bio Epitranscriptomics M6anet AnalysisDetect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immunoprecipitation.Votes: 0GitHub stars: 2
- Bio Differential Expression Batch CorrectionRemove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.Votes: 0GitHub stars: 2
- Bio De ResultsExtract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.Votes: 0GitHub stars: 2