12,425 skills found · Page 185 of 415
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 / 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 c…
FreedomIntelligence / arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3)
FreedomIntelligence / arxiv-searchSearch arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
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)…
FreedomIntelligence / binder-designGuidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types.
FreedomIntelligence / bio-alignment-filteringFilter alignments by flags, quality, and regions using samtools and pysam.
FreedomIntelligence / bio-alignment-indexingCreate indices for random access to alignment files using samtools and pysam.
FreedomIntelligence / bio-alignment-pairwisePerform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner
FreedomIntelligence / bio-alignment-sortingSort alignment files by coordinate or read name using samtools and pysam.
FreedomIntelligence / bio-alignment-validationPost-alignment quality control to verify alignment quality and identify issues.
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-batch-downloadsDownload large numbers of records from NCBI efficiently using the history server, batching, and proper rate limiting.
FreedomIntelligence / bio-blast-searchesRun BLAST searches against NCBI databases using Biopython's Bio.Blast module.
