1,133 skills found · Page 19 of 38
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / 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
FreedomIntelligence / bio-imaging-mass-cytometry-phenotypingCell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches
FreedomIntelligence / bio-imaging-mass-cytometry-spatial-analysisSpatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing
FreedomIntelligence / bio-immunoinformatics-epitope-predictionPredict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens
FreedomIntelligence / bio-immunoinformatics-immunogenicity-scoringScore and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design
FreedomIntelligence / bio-immunoinformatics-mhc-binding-predictionPredict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences
FreedomIntelligence / bio-cfdna-preprocessingPreprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering
FreedomIntelligence / bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner
FreedomIntelligence / bio-atac-seq-differential-accessibilityFind differentially accessible chromatin regions between conditions using DiffBind or DESeq2
FreedomIntelligence / bio-atac-seq-footprintingDetect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS
FreedomIntelligence / bio-blast-searchesRun BLAST searches against NCBI databases using Biopython's Bio.Blast module.
FreedomIntelligence / bio-clinical-databases-clinvar-lookupQuery ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF
FreedomIntelligence / bio-clinical-databases-gnomad-frequenciesQuery gnomAD for population allele frequencies to assess variant rarity
FreedomIntelligence / bio-clinical-databases-hla-typingCall HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications
FreedomIntelligence / bio-clinical-databases-myvariant-queriesQuery myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request
FreedomIntelligence / bio-clinical-databases-pharmacogenomicsQuery PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines
FreedomIntelligence / bio-clinical-databases-polygenic-riskCalculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics
FreedomIntelligence / bio-clinical-databases-tumor-mutational-burdenCalculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds
FreedomIntelligence / bio-clinical-databases-variant-prioritizationFilter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis
FreedomIntelligence / bio-codon-usageAnalyze codon usage patterns and calculate codon adaptation metrics using Biopython.
