3,638 skills found · Page 49 of 122
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-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 / 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 / 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-crispr-screens-base-editing-analysisAnalyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies
FreedomIntelligence / bio-format-conversionConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO
FreedomIntelligence / bio-fastq-qualityWork with FASTQ quality scores using Biopython
Agentchengfeng / chengfeng-check-updates剪辑环境的唯一管理者：就绪检查（skills 是否最新 → Runtime 是否配套）、Skills 更新激活、Runtime 安装与体检。用户说检查更新、安装剪辑环境、装播放器、检查剪辑环境、剪辑环境就绪了吗、配置转录凭证时使用；业务 Skill（剪口播/字幕/画面/导出）第 0 步也引用本 Skill 的就绪检查。不用于剪辑、字幕、画面、导出本身或项目数据迁移。
Agentchengfeng / chengfeng-cut剪辑中文口播原素材：逐词转录、词典修字出修字表、五轮扫描找口误与重复、汇总表与重复句子表、打开 Studio 让用户复核、复盘沉淀用户偏好与词典。只产出一份已复核的删词账本，不切媒体、不做字幕、不做分镜动画。用户说剪口播、处理口误、生成口播基础素材、继续剪口播，或确认卡回传 action=return_cut_review 时使用。不要用于执行物理剪切、导出剪后视频、单独安装、单独打开工作台或口播分镜成片。
