12,235 skills found · Page 179 of 408
FreedomIntelligence / bio-epidemiological-genomics-transmission-inferenceInfer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data
FreedomIntelligence / bio-epidemiological-genomics-variant-surveillanceAssign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern
FreedomIntelligence / bio-flow-cytometry-bead-normalizationBead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization
FreedomIntelligence / bio-flow-cytometry-clustering-phenotypingUnsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows
FreedomIntelligence / 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
FreedomIntelligence / bio-flow-cytometry-doublet-detectionDetect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods
FreedomIntelligence / bio-fragment-analysisAnalyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection
FreedomIntelligence / 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)
FreedomIntelligence / bio-genome-assembly-metagenome-assemblyMetagenome assembly reconstructs genomes from mixed microbial communities. Long reads enable recovery of complete circular genomes and resolution of strain-level differences.
FreedomIntelligence / bio-genome-engineering-base-editing-designDesign guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks
FreedomIntelligence / bio-genome-engineering-grna-designDesign guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models
FreedomIntelligence / bio-genome-engineering-hdr-template-designDesign homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms
FreedomIntelligence / bio-genome-engineering-off-target-predictionPredict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity
FreedomIntelligence / bio-genome-engineering-prime-editing-designDesign pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks
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
