All nodes (119)

Load an .h5ad file into AnnData.

1 params

Load 10X Genomics HDF5 (.h5) from Cell Ranger output.

2 params

Load 10X Genomics MTX directory (matrix.mtx + features + barcodes).

3 params

Load a CSV/TSV expression matrix (cells × genes).

4 params

Load a Loom file. Use Load Velocyto Loom for RNA velocity layers.

2 params

Load a generic text expression matrix.

4 params

Load a velocyto .loom for RNA velocity (spliced/unspliced/ambiguous layers).

1 params

Load STARsolo Velocyto MTX directory (spliced/unspliced/ambiguous).

1 params

Load single-molecule transcript locations (Xenium / MERFISH / seqFISH) into adata.uns["transcripts"].

7 params

Concatenate multiple AnnData objects with per-input labels and live pre-merge preview.

6 params

Attach external metadata CSV/TSV/Excel to adata.obs with auto-match suggestions and live match-rate preview.

8 params

Filter cells or genes using multi-condition AND/OR builder with live preview.

4 params

Assign cells to custom categorical groups via multi-condition rules; same label across groups acts as OR.

4 params

Split cell IDs by delimiter into new obs columns (e.g. B_cac10_AAACCTGAG → type/patient/barcode).

3 params

Browse adata.obs and apply small obs edits (drop / rename / dtype convert) in one node. Dedicated UI: multi-select autocompletes, rename pair editor, inline obs preview table, per-column summary accordion (dtype, n_unique, n_missing, value_counts top N bar chart, sample uniques).

7 params

Save AnnData to .h5ad.

2 params

Export analysis results to CSV — 15 export types (markers, pathway, obs, var, lineage_drivers, fate_probabilities, cpdb, bulk_de, gsea, atac_*, dmp, dmr, transcripts, xenium).

8 params

Filter cells/genes by QC metrics. Unified node (replaces qcMetrics + qcVisualization).

33 params

Normalize total counts per cell (scanpy normalize_total).

5 params

log(x+1) transformation. Run after Normalize, before HVG/PCA.

5 params

Identify highly variable genes (HVGs) that drive biological variation.

10 params

Scale to unit variance and zero-center. Required before PCA. Auto-saves adata.raw.

4 params

Detect doublets using Scrublet. Run early in the pipeline.

6 params

Principal Component Analysis — required before Neighbors/UMAP/Harmony.

7 params

k-nearest neighbor graph on PCA space. Required for clustering and UMAP.

6 params

UMAP 2D embedding for visualization. Local neighborhood structure preserved; global distances are NOT meaningful.

8 params

t-SNE embedding (alternative to UMAP). Good for distinct clusters; slower than UMAP.

6 params

Leiden or Louvain community detection on the kNN graph, or K-Means with a fixed number of clusters on the embedding.

9 params

Rename or merge cluster labels for cell type annotation.

4 params

Differential expression — ranks all genes per cluster (Wilcoxon by default). Replaces "Find Markers" naming.

12 params

Harmony batch correction — outputs to obsm["X_pca_harmony"]. Set use_rep="X_pca_harmony" in Neighbors after.

10 params

Partition-based Graph Abstraction — coarse-grained trajectory topology between clusters.

3 params

Diffusion Pseudotime — orders cells along a continuous trajectory (0 = root, 1 = differentiated).

6 params

Diffusion map embedding — captures continuous transitions. Required before DPT.

1 params

Force-directed graph layout (ForceAtlas2 / Fruchterman-Reingold).

4 params

Estimate RNA velocity from spliced/unspliced counts (scvelo).

6 params

Compute velocity transition graph for stream/arrow plots.

3 params

Latent time from dynamical RNA velocity. More accurate than DPT when velocity available.

3 params

Identify terminal/initial states from velocity transition matrix.

2 params

Compute cell-cell transition probabilities (Markov chain). Kernel: cytotrace / pseudotime / velocity / connectivity.

5 params

GPCCA — identify terminal/initial macrostates and compute fate probabilities.

7 params

Identify genes driving differentiation toward each cell fate (correlation with fate probabilities).

5 params

Plot fate analysis results (fate probs, macrostates, terminal/initial states, circular projection, coarse transition, lineage drivers).

4 params · 7 plot types

GAM-smoothed expression trends along differentiation lineages.

4 params · 2 plot types

LLM-based cell type annotation (OpenAI / Anthropic / Gemini). No reference dataset needed.

10 params

Reference-based label transfer via kNN mapping on joint PCA.

7 params

Per-cell type annotation using CellTypist pretrained logistic-regression models — no LLM and no custom reference required.

6 params

Compare 2+ categorical annotation/cluster columns and visualise their agreement — a QC step to judge whether an automatic annotation can be trusted.

13 params · 2 plot types

Extract top N DEG genes per cluster as a deduplicated gene list (renamed from "Extract Gene List").

7 params

GO/KEGG enrichment per cluster using gseapy + Enrichr REST API.

8 params

Infer the activity of 14 signalling pathways from signed downstream expression footprints.

11 params

Score 50 MSigDB Hallmark biological programs from the expression matrix.

10 params

Infer transcription-factor activity from curated, signed TF-target regulons.

10 params

Cell-cell ligand-receptor interaction analysis. Modes: "run" (in-app) or "load" (read existing CLI output).

9 params

Visualize CellPhoneDB results — heatmap (interaction counts), dotplot (LR pairs for specific cell types), or chord (network).

9 params · 3 plot types

Consensus ligand-receptor scoring (rank_aggregate) combining CellPhoneDB, NATMI, Connectome, logFC and more into one ranking of interactions between cell groups.

5 params

Dotplot of LIANA consensus ligand-receptor results — dot size = interaction specificity, colour = expression magnitude.

11 params · 1 plot types

UMAP/t-SNE/PCA scatter colored by metadata or gene expression.

21 params

PCA elbow (variance ratio), scatter, loadings, overview.

9 params · 4 plot types

Cluster composition, proportions, embedding overlay, dendrogram.

7 params · 5 plot types

Heatmap, dotplot, violin, stacked violin, matrixplot, tracksplot, volcano of marker genes.

20 params · 11 plot types

Highly variable gene dispersion plot.

11 params

Histogram, scatter, embedding overlay of doublet detection results.

8 params · 3 plot types

PAGA graph, DPT pseudotime, diffusion map, draw_graph plots.

11 params · 6 plot types

Stream, arrow, phase portrait, speed, coherence, latent time.

15 params · 8 plot types

Enrichr GO/KEGG enrichment as barplot or dotplot.

6 params · 2 plot types

Add spatial X/Y from CSV/TSV directly to obsm["spatial"]. Has its own loader — no Load CSV needed.

7 params

Filter low-density spatial regions (Xenium edges, bubbles, control probe noise) using a grid.

4 params

Lasso/box-select tissue regions and label them as obs categorical column. Replaces spatialInteractiveViewer.

4 params

Read-only interactive Plotly WebGL scatter. Color by obs column or gene, select with lasso, box or polygon, highlight groups, inspect stats — all without modifying adata.

4 params

Spatial neighbor graph based on physical coordinates. Required for all spatial statistics.

8 params

Test if cell types co-localize or avoid each other (squidpy nhood_enrichment).

3 params

Spatial co-occurrence at multiple distances.

6 params

Moran's I, Geary's C, or sepal diffusion time — identifies spatially variable genes (SVGs).

7 params

Reads a whole 10x Visium SpaceRanger folder — counts, real coordinates, true scalefactors, and the H&E image.

6 params

Reads a 10x Xenium cell-feature matrix with its aligned micron centroids, without pulling in whole-slide morphology images.

4 params

Loads one chosen square-bin resolution from a Visium HD run, with a bin-count guard applied before anything is read into memory.

9 params

Loads Vizgen MERSCOPE cell-by-gene counts with their metadata, micron coordinates, and optional coordinate transformation.

5 params

Loads flat NanoString CosMx exports, using slide-wide global coordinates as the canonical spatial system.

10 params

Reports the observed contact matrix between clusters plus each cluster's network role on the spatial graph.

3 params

Estimates the cell-type mixture inside each spot with a transparent non-negative least-squares fit against a labelled reference.

9 params

Extracts per-spot intensity, histogram, and texture descriptors from the tissue image already attached to the data.

10 params

Finds spatially autocorrelated genes and groups them into coordinated local-expression modules using Hotspot.

13 params

Scores ligand-receptor pairs per spot against the spatial graph, mapping where signalling is co-located.

8 params

Segments tissue into contiguous domains by blending each cell's expression with its physical neighbours.

10 params

Groups cells by the mix of cell types surrounding them, revealing recurring tissue microenvironments.

7 params

Ripley's L/F/G statistics — measures spatial clustering patterns.

9 params

L-R interaction analysis using squidpy ligrec (CellPhoneDB-like permutations).

4 params

Spatial scatter and analysis overlays (nhood, co-occurrence, ripley, autocorr, ligrec).

31 params · 16 plot types

Load a generic bulk count matrix (CSV/TSV/H5AD). Genes × samples typically — enable Transpose.

4 params

featureCounts .txt or STAR ReadsPerGene.out.tab. Auto-handles header lines and STAR strand selection.

4 params

Load Kallisto abundance.tsv or Salmon quant.sf. Format auto-detected. Single-file loader; merge per-sample with Merge Data.

7 params

Sample-level QC — library size, gene count, IQR-based outlier detection.

4 params

CPM / TMM / DESeq2 size-factor / VST. Raw counts always saved to layers["counts"].

4 params

Remove lowly expressed genes (e.g. CPM > 1 in ≥2 samples).

7 params

PyDESeq2 differential expression between two conditions (t-test fallback).

8 params

Bulk pathway enrichment (gseapy) — preranked GSEA or ORA.

11 params

Volcano, MA, DEG heatmap, sample distance, library size.

11 params · 7 plot types

Load Illumina methylation IDAT (450K / EPIC v1 / EPIC v2 / Mouse). EPIC v2 auto-routes to mepylome (methylprep ceiling).

8 params

Load pre-processed beta-value matrix (CSV/TSV/TXT). Used when raw IDAT is unavailable.

8 params

Per-sample / per-probe call rates with a built-in QC plot. "label" or "filter" mode.

15 params

NaN-aware between-array quantile normalization in beta space, or no-op. Raw-signal NOOB/SWAN preprocessing belongs in Load IDAT.

2 params

Drop SNP-associated, sex chromosome, cross-reactive, low call rate probes. Mandatory before DMP.

8 params

Differentially Methylated Position — vectorized Welch's t-test or limma-style moderated t-test.

9 params

Multi-group (3+) differential methylation — omnibus moderated F-test (empirical-Bayes shrinkage, limma-style) plus a reference contrast per group. Pure numpy, not R limma.

7 params

Differentially Methylated Regions (Bumphunter-style) — groups adjacent same-direction DMPs within max_gap_bp.

6 params

Fisher enrichment of significant DMPs against local BED or cached ENCODE SCREEN cCRE classes, with BH FDR and a 95% CI forest plot.

22 params

Genomic-coordinate Manhattan, capped/raw QQ and volcano, top/random/most-variable heatmap up to 10,000 probes, and direction-aware annotation distributions plus existing methylation plots.

29 params · 10 plot types

Genome-browser-style locus plot for one DMR — per-sample beta + group means, DMR span shaded.

12 params

CpG-bias-corrected gene-set enrichment for DMP results (gometh-style two-step).

15 params

Cell Ranger ATAC MEX directory (matrix.mtx + peaks.bed + barcodes.tsv).

2 params

Build peak×cell matrix from 10X fragments.tsv.gz. Calls peaks if no BED provided.

8 params

Load pre-computed peak×cell matrix (CSV or H5AD).

3 params

Per-cell QC — total fragments, peaks, FRIP score.

4 params

Call peaks with MACS3 (or top-N accessible regions fallback).

4 params

Latent Semantic Indexing (TF-IDF + randomized SVD). Standard ATAC dim-reduction.

4 params

Differential chromatin accessibility between two cell groups (t-test + FDR).

7 params

TF motif enrichment in differentially accessible peaks via JASPAR / pyjaspar.

6 params

FRIP bar, fragment size, peak accessibility heatmap, ATAC UMAP, differential volcano.

3 params · 6 plot types