Scanpy end-to-end
QC filtering, normalization, HVG selection, PCA, Leiden clustering, UMAP, marker genes.
Seurat integration
Multi-dataset harmonization with SCTransform and Harmony — batch correction done right.
Cell-type annotation
Automated annotation with CellTypist + manual marker review in a reproducible notebook.
scVelo RNA velocity
Dynamical and stochastic velocity models with arrow overlays on your UMAP.
Doublet detection
Scrublet on each sample separately, with automatic threshold selection and QC plots.
CellChat communication
Ligand-receptor inference across cell types, with circos and heatmap visualizations.
DESeq2 differential expression
Count modelling with shrinkage, LFC estimates, dispersion plots, and volcano output.
PyDESeq2
Pure-Python DESeq2 reimplementation — perfect for HPC where R envs are painful.
STAR + Salmon quantification
Two-pass STAR alignment plus Salmon quant with decoy-aware index, wrapped in Snakemake.
GSEA enrichment
Pre-ranked GSEA with MSigDB hallmark, C5, and custom gene sets. Tidy tables + plots.
Visium / 10x spatial
Space Ranger outputs → Scanpy/Seurat spatial object → spot clustering and niches.
cell2location deconvolution
Reference scRNA → spatial cell-type abundance maps with Bayesian uncertainty.
Xenium / MERFISH
Subcellular-resolution ingestion, cell-boundary QC, and spatial neighborhood analysis.
CellPose segmentation
Cell-boundary masks with Cyto, Nuclei, or custom-trained models; GPU-aware.
StarDist nuclei
Shape-aware star-convex polygon detection for dense nuclei in IF / IHC / DAPI.
DeepCell tissue
Whole-tissue Mesmer segmentation for multiplexed IF (CODEX, MIBI, IMC).
ATAC-seq pipeline
Trim, align with bowtie2, call peaks with MACS2, annotate, and compute FRiP / TSS.
ChIP-seq pipeline
Broad or narrow peak calling with MACS2; deepTools bigWig QC; motif enrichment.
CUT&RUN / CUT&Tag
Low-input chromatin profiling with SEACR peak calling and spike-in normalization.
scATAC-seq (ArchR)
Tile matrix, gene-score inference, peak-to-gene linkage, and motif footprinting.
JASPAR motif enrichment
TF-binding-site enrichment in peak sets with JASPAR PFMs + HOMER backups.
AlphaFold lookup
Fetch predicted structure by UniProt ID, visualize pLDDT, align homologs.
PyMOL scripts
Batch structural rendering with publication-ready ray-traced images.
Biopython toolkit
FASTA/PDB parsing, BLAST, multiple-sequence alignment, phylogeny helpers.
PubMed literature
Search NCBI E-utilities, retrieve abstracts, cite DOIs inline during chat sessions.
GEO datasets
Query GSE / GSM accessions, pull metadata, stream count matrices to disk.
GTEx expression
Tissue-specific gene expression and eQTL lookup across the GTEx v8 release.
KEGG pathways
Pathway enrichment and gene-ontology crosswalks — human, mouse, more.
Gene annotation
Cross-species ortholog lookup, Ensembl ↔ RefSeq ↔ HGNC resolution.
LatchBio integration
Submit and track workflows on Latch's cloud-native bioinformatics platform.
Enhanced volcano plot
Publication-ready volcano plots with labeled hits, thresholds, and custom styling.
UMAP projections
Tune n_neighbors, min_dist, and seed for reproducible embeddings.
Matplotlib / seaborn
Lab-branded style sheets for consistent figures across manuscripts and grants.
ComplexHeatmap
Multi-annotation heatmaps with dendrograms, splits, and composite color bars.
HuggingFace transformers
Fine-tune or run inference with Geneformer, scGPT, and other biology-domain LLMs.
scVI probabilistic models
Latent-space modelling for batch correction, differential expression, and imputation.
PyTorch training loops
GPU-aware templates — DataLoader, mixed precision, checkpointing, W&B logging.
Don't see what you need? Ask the agent — it can write any protocol on demand.
