3,616 skills found ¡ Page 48 of 121
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-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-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-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-neoantigen-predictionIdentify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses
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 / alphafoldValidate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain câĻ
FreedomIntelligence / bindcraftEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5)âĻ
FreedomIntelligence / bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner
FreedomIntelligence / bio-atac-seq-atac-peak-callingCall accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters
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-atac-seq-motif-deviationAnalyze transcription factor motif accessibility variability using chromVAR
FreedomIntelligence / bio-atac-seq-nucleosome-positioningExtract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis
FreedomIntelligence / bio-chipseq-super-enhancersIdentifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools
FreedomIntelligence / bio-compressed-filesRead and write compressed sequence files (gzip, bzip2, BGZF) using Biopython
FreedomIntelligence / bio-consensus-sequencesGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus
FreedomIntelligence / bio-filter-sequencesFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython
FreedomIntelligence / bio-flow-cytometry-compensation-transformationSpillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms
FreedomIntelligence / bio-flow-cytometry-differential-analysisDifferential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods
FreedomIntelligence / bio-flow-cytometry-fcs-handlingRead and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration
FreedomIntelligence / bio-imaging-mass-cytometry-quality-metricsQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC
FreedomIntelligence / bio-isoform-switchingAnalyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions
FreedomIntelligence / bio-long-read-sequencing-isoseq-analysisAnalyze PacBio Iso-Seq data for full-length isoform discovery and quantification
