End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data. — from bg-szy/TOP-SKILLS
Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.
Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing — from…
Infer orthologous gene groups across species using OrthoFinder and ProteinOrtho. Identify orthologs, paralogs, and co-orthologs for comparative genomics and functional annotation…
Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures.
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into…
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data.
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines.
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation.
AI-powered multimodal fusion of radiology (CT/MRI/PET) and pathology (H&E/IHC) imaging with clinical and genomic data for comprehensive cancer diagnostics and treatment prediction.
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downs — from…
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcripto — from…
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery.
Multi-omic biomarker discovery studio that ingests expression + metadata, performs QC, multi-strategy feature selection, nested CV model training, survival analysis hooks, and…
End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, variant calling, filtering, and annotation for cancer — from…
AI-powered multimodal diagnostic fusion integrating radiology imaging (CT/MRI/PET), digital pathology (WSI), genomics, and clinical data for comprehensive cancer diagnosis and…
Geometric deep learning-based polygenic risk score prediction using PRS-Net for modeling gene interactions, enhanced disease prediction, and cross-ancestry portability.
Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels.
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are need — from…
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill.
Access UniProt protein database for sequences, annotations, and functional information. Use when retrieving protein data, GO terms, domain annotations, or protein-protein…
Implements Manus-style file-based planning for complex tasks. Creates task_plan.md, findings.md, and progress.md.
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches.
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies…
An AI agent for therapeutic discovery that executes transparent, multi-step omics analyses including research planning, code execution, and literature reasoning.
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream ana — from…
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visual — from…
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit — from…
End-to-end spatial transcriptomics workflow for Visium/Xenium data. Covers data loading, preprocessing, spatial analysis, domain detection, and visualization with Squidpy — from…
Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and — from…
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies.
AI-powered myeloproliferative neoplasm monitoring for disease progression prediction, treatment response tracking, and transformation risk assessment in PV, ET, and myelofibrosis.
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy.
Detect positive selection using dN/dS (omega) tests with PAML codeml and HyPhy. Identify sites and branches under adaptive evolution through codon models and branch-site tests.
Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV.
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac.
Create Firecrawl monitors that watch pages, sites, or web search results and send change alerts by email or webhook.
Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts.
Parse trial protocols and patient data to produce criterion-level MET/NOT/UNKNOWN determinations with evidence and gaps for clinical trial screening tasks.
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and r — from…
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV.
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis.
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto. — from bg-szy/TOP-SKILLS
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or — from…
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes.
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation — from…
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments. — from bg-szy/TOP-SKILLS
Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.
Calculates and harmonizes Tumor Mutational Burden (TMB) across platforms to predict immunotherapy response.
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps.
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping — from…
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython.
AI-powered PROTAC (Proteolysis Targeting Chimera) design for targeted protein degradation, integrating ternary complex prediction, linker optimization, and ADMET modeling.
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.
End-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differentia — from…
End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation. — from bg-szy/TOP-SKILLS
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations.
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type pro — from…