Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that actually work for neurodivergent minds.
EnglishA multimodal precision oncology agent leveraging GPT-4 and vision transformers for cancer diagnosis, biomarker detection, and treatment planning.
EnglishFilter alignments by flags, mapping quality, and regions using samtools view and pysam.
EnglishCreate and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
EnglishSort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
EnglishValidate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.
EnglishGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus.
EnglishAssess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
EnglishSpecies abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates.
EnglishDetect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants.
EnglishDeep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data.
EnglishJoint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR.
EnglishEnd-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting.
EnglishAnalyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology frameworks.
EnglishAI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images.
EnglishUse omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction…
EnglishTurn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality…
EnglishWalk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
EnglishGuide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment.
EnglishAssist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub…
EnglishExtend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating…
EnglishAI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilities for therapeutic targeting.
EnglishAI-guided CAR-T cell design for solid tumors using antigen prioritization, safety-by-design architectures, and exhaustion-resistant engineering.
English
AGENT SKILLS ATLASIncludes Adhd Daily Planner, Autonomous Oncology Agent, Bio Alignment Filtering, and other workflows.
Claude Code
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GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Adhd Daily Planner
Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that actually work for neurodivergent minds.
Autonomous Oncology Agent
A multimodal precision oncology agent leveraging GPT-4 and vision transformers for cancer diagnosis, biomarker detection, and treatment planning.
Bio Alignment Filtering
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting
Bio Alignment Indexing
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
Bio Alignment Sorting
Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.
Bio Alignment Validation
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment da
Bio Consensus Sequences
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructi
Bio Gatk Variant Calling
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality sc
Bio Genome Assembly Assembly Qc
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when
Bio Metagenomics Abundance
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate
Bio Metagenomics Amr Detection
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resis
Bio Variant Calling Deepvariant
Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling var
Bio Variant Calling Joint Calling
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when
Bio Workflows Atacseq Pipeline
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIA
Biologist Analyst
Analyzes living systems and biological phenomena through biological lens using evolution, molecular biology, ecology, and systems biology frameworks. Provides insights on
Bone Marrow AI Agent
AI-powered bone marrow morphology analysis, cell classification, and hematologic disorder diagnosis using deep learning on aspirate and biopsy images.
Bulk Rna Seq Batch Correction with Combat
Use omicverse's pyComBat wrapper to remove batch effects from merged bulk RNA-seq or microarray cohorts, export corrected matrices, and benchmark pre/post correction visu
Bulk Rna Seq Deconvolution with Bulk2single
Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality contro
Bulk Rna Seq Deseq2 Analysis with Omicverse
Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
Bulk Rna Seq Differential Expression with Omicverse
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. U
Bulk Wgcna Analysis with Omicverse
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes
Bulktrajblend Trajectory Interpolation
Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq, training beta-VAE and GNN models, and interpolating mis
Cancer Metabolism Agent
AI-powered analysis of cancer metabolic reprogramming including Warburg effect, glutamine addiction, lipid metabolism, and metabolic vulnerabilities for therapeutic targeting.
Cart Design Optimizer Agent
AI-guided CAR-T cell design for solid tumors using antigen prioritization, safety-by-design architectures, and exhaustion-resistant engineering.
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