AI Agent Workflow Collection

Skill pack

AGENT SKILLS ATLAS

AI Agent Workflow Collection

Includes Bio Alignment Bam Processing, Bio Epigenomics Regulation, Bio Genome Assembly Annotation, and other workflows.

Install with

Claude Code

Codex

Cursor

GitHub Copilot

Gemini CLI

Supported by the Atlas install prompt. Skill-specific requirements vary.

Pack stats

Skills64CategorygeneralStars0

What’s included

Bio Alignment Bam Processing

比对文件处理 skill。用于 STAR/BWA/Bowtie2/HISAT2/minimap2 输出后的 SAM/BAM/CRAM sort、index、filter、dedup、coverage、mapping QC、read group、region extraction 和 pysam/samtools 操作设计。

Bio Epigenomics Regulation

表观组学与调控分析 workflow skill。用于 ATAC-seq、ChIP-seq、CUT&Tag、methylation、Hi-C、CLIP-seq、motif、peak calling、differential binding、TAD、loop、GRN/SCENIC 等任务。

Bio Genome Assembly Annotation

基因组组装、注释和比较基因组 workflow skill。用于 short-read/long-read/HiFi assembly、polishing、scaffolding、BUSCO、contamination、Prokka、eukaryotic gene prediction、repeat/ncRNA/functional annotation、ortholog、synteny、selection 等任务。

Bio Immune Repertoire Neoantigen

免疫信息学 workflow skill。用于 TCR/BCR repertoire、VDJ、clonotype、MIXCR、scirpy、neoantigen prediction、MHC binding、epitope、immunogenicity scoring、tumor variant 到 neoantigen 等任务。

Bio Long Read Sequencing Analysis

长读长测序分析 workflow skill。用于 Nanopore 或 PacBio 的 basecalling、read QC、long-read alignment、SV calling、Iso-Seq、direct RNA、nanopore methylation、phasing、assembly polishing 和长读长交付。

Bio Mass Spectrometry Toolkit

质谱分析工具 skill。用于 PyOpenMS、OpenMS、matchms、mzML/mzXML、feature detection、RT alignment、spectral similarity、peptide/protein identification、metabolite annotation 和 MS 数据结构处理。

Bio Population Genetics Gwas

群体遗传与 GWAS skill。用于 PLINK/VCF QC、PCA、admixture、LD pruning、association testing、GWAS summary stats、selection statistics、Manhattan/QQ、Fst、Tajima D、iHS 和 XP-EHH 交接。

Bio Post Transcriptional Regulation

转录后调控 workflow skill。用于 alternative splicing、differential splicing、Ribo-seq、small RNA/miRNA、CLIP-seq/RBP binding、m6A/epitranscriptomics、RNA modification calling 和 RNA 调控可视化交接。

Bio Proteomics Metabolomics

蛋白质组、代谢组、脂质组和质谱数据 workflow skill。用于 mzML/mzXML、DDA/DIA、peptide identification、protein inference、differential abundance、PTM、XCMS、MS-DIAL、feature alignment、metabolite annotation 等任务。

Bio Regulatory Annotation Databases

调控注释数据库 skill。用于 ENCODE、ReMap、Cistrome、JASPAR、RegulomeDB、Roadmap Epigenomics、UCSC/Genome Browser tracks、TF motif、peak set 和 enhancer/promoter 注释查询交接。

Bio Variant Calling Interpretation

变异检测与解释 workflow skill。用于 germline/somatic SNP/indel、CNV、SV、long-read variant、VCF 过滤注释、ClinVar/gnomAD/COSMIC 查询、GATK/BCFtools/DeepVariant/Mutect2/CNVkit 等任务。

Bio Assay Image Quantification

实验图像定量 skill。用于 Western blot、gel electrophoresis、dot blot、plate image 等 band/lane/spot 定量、背景扣除、housekeeping/loading control 归一化、重复聚合和图表交接。

Bio Bioimage Segmentation

生物显微图像分割与定量 skill。用于荧光、明场、相差、3D z-stack 或 time-lapse 图像的 Cellpose、scikit-image、OpenCV、napari 审阅、mask 生成、regionprops 和细胞追踪交接。

Bio Biology Datapipes Adapters

OneScience 生信 datapipe 和 adapter skill。用于 biology/protenix/simplefold/openfold/evo2 数据读取、FASTA/MSA/PDB/mmCIF/JSON/SMILES 到模型 batch 的桥接、adapter registry、ProtenixInferAdapter、GenomeDataset 和输入协议兼容性判断。

Bio Biomarker Machine Learning

组学生物标志物机器学习 skill。用于高维 omics classifier、feature selection、nested CV、batch-aware split、survival analysis、SHAP/LIME 解释、模型卡和验证报告交接。

Bio Causal Genomics

因果基因组学 skill。用于 Mendelian randomization、colocalization、fine mapping、pleiotropy、Steiger filtering、mediation、eQTL/mQTL/pQTL 与 GWAS 信号整合和敏感性分析交接。

Bio Cell Imaging Cytometry

细胞图像、流式与空间表型范畴路由。用于 FCS 流式或质谱流式、门控、补偿、CyTOF/IMC、显微图像分割、全切片病理图像、OMERO 或 Bio-Formats 图像管理、细胞表型和空间邻域分析。

Bio Comparative Genomics Evolution

比较基因组与进化分析 skill。用于 ortholog inference、synteny、whole-genome duplication、positive selection、dN/dS、HGT、ancestral reconstruction、annotation transfer 和跨物种功能比较。

Bio Crispr Guide Editing

CRISPR guide 与编辑实验设计 skill。用于 sgRNA、Cas9/Cas12a、CRISPRa/i、base editing、prime editing、HDR donor、off-target 过滤、编辑窗口和验证引物交接。

Bio Digital Pathology Wsi

全切片病理图像 WSI 处理 skill。用于 H&E/IHC/mIF whole-slide image 的组织检测、tile extraction、stain normalization、slide QC、tile-level 特征、病理 ML 数据集准备和报告交接。

Bio Experimental Design Power

生物实验设计、样本量和统计功效 skill。用于 omics study design、批次设计、paired/blocking、replicate、power analysis、multiple testing、randomization、covariate、time course 和统计风险评估。

Bio Expression Matrix Feature Tables

表达矩阵、特征表和稀疏组学矩阵基础 skill。用于 count matrix、TPM/CPM、feature x sample 表、gene ID mapping、metadata join、sparse Matrix Market、AnnData h5ad、loom、zarr 和下游 workflow 输入检查。

Bio Flow Cytometry Analysis

流式和质谱流式分析 skill。用于 FCS 文件读取、通道元数据、补偿矩阵、arcsinh/logicle 转换、QC、doublet/dead cell 过滤、手动或自动门控、聚类表型和差异丰度分析。

Bio Functional Genomics Screens

功能基因组筛选 workflow skill。用于 pooled CRISPR screen、RNAi screen、Perturb-seq、DepMap/gene essentiality、sgRNA count matrix、MAGeCK 风格 hit calling、library QC 和候选基因优先级交接。

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