Vol. 01 · No. 1 · Beta EditionOCT 10, 2026

Node catalog

119 nodes. 5 modalities. One canvas.

This is the app’s Node Library, in the same order it appears on screen: pick a modality, walk the stages from loading to plots, and click any node for its parameters. Nodes that serve several modalities — Quality Control, Merge Cell Meta, Export CSV — appear in each of them.

119

Nodes

14

Categories

5

Modalities

22

Loaders

93

Plot types

33

Templates

Type to search all 119 nodes. Results link to the node’s parameter reference.

By modality

Pipeline order, as the app shows it.

Each stage below is a section of the app’s Node Library. Stages marked collapsed start folded in the app — utilities, export and the trajectory family — and open with one click.

scRNA-seq

Single-cell RNA-seq

Drop-seq, 10x, Smart-seq — anything with genes × cells.

66
nodes: 8
loaders: 54
plot types: 20
templates

scRNA-seq solution 20 templates

01
Load Data
8 nodes
Load H5AD Load 10X H5 Load 10X MTX Load CSV / TSV Load Loom Load Text Load Velocyto Loom Load STARsolo Velocity
02
QC & Preprocessing
6 nodes
Quality Control Doublet Detection Normalize Log1p Highly Variable Genes Scale
03
Dimensionality Reduction & Integration
5 nodes
PCA Harmony Neighbors UMAP t-SNE
04
Clustering & Annotation
6 nodes
Clustering Edit Clusters Auto Annotation CellTypist Annotation Cell Mapper Annotation Concordance2 plots
05
DEG & Pathways
7 nodes
DEG Analysis Top DEG Gene List Pathway Enrichment GSEA / ORA PROGENy Activity Hallmark Activity CollecTRI TF Activity
06
Cell–Cell Communication
2 nodes
CellPhoneDB LIANA
07
Trajectory & Velocity
11 nodescollapsed
Diffusion Map PAGA DPT Draw Graph RNA Velocity Velocity Graph Latent Time Terminal States CellRank Kernel Cell Fate Analysis Lineage Drivers
08
Plots
13 nodes
Embedding Plot Cluster Visualization5 plots Marker Visualization11 plots HVG Visualization PCA Visualization4 plots Doublet Visualization3 plots Trajectory Visualization6 plots Velocity Visualization8 plots CellRank Visualization7 plots Gene Trends2 plots Pathway Visualization2 plots CellPhoneDB Plot3 plots LIANA Plot1 plot
09
Utilities & Export
8 nodescollapsed
Merge Data Merge Cell Meta Subset Data Define Groups Split Cell ID Obs Inspector Save H5AD Export CSV

Spatial

Spatial transcriptomics

Visium, MERFISH, Xenium — single-cell data that also has spatial coordinates per cell.

50
nodes: 10
loaders: 16
plot types: 4
templates

Spatial solution 4 templates

01
Load Data
11 nodes
Load Visium (SpaceRanger)Load Visium HD Load Xenium Load MERSCOPE Load CosMx Load Transcripts Add Coordinates Load H5AD Load 10X H5 Load 10X MTX Load CSV / TSV
02
QC & Preprocessing
7 nodes
Spatial Density QC Spatial Image Features Quality Control Normalize Log1p Highly Variable Genes Scale
03
Clustering & Embedding
6 nodes
PCA Harmony Neighbors UMAP Clustering Edit Clusters
04
Cell Type Annotation
3 nodescollapsed
Auto Annotation CellTypist Annotation Cell Mapper
05
Interactive Viewer
2 nodes
Spatial Viewer Spatial Grouping
06
Neighborhood & Interaction
6 nodes
Spatial Neighbors Nhood Enrichment Spatial Graph Statistics Co-Occurrence Ligand-Receptor Spatial Ligand-Receptor
07
Tissue Structure
3 nodes
Spatial Domains (BANKSY)Cellular Neighborhood Spot Deconvolution (NNLS)
08
Spatial Statistics
3 nodes
Spatial Autocorrelation Spatial Hotspot Ripley
09
Plots
2 nodes
Spatial Visualization16 plots Embedding Plot
10
Utilities & Export
7 nodescollapsed
Merge Cell Meta Subset Data Define Groups Split Cell ID Obs Inspector Save H5AD Export CSV

Bulk RNA-seq

Bulk RNA-seq

Count matrices, featureCounts, kallisto / salmon abundance — samples × genes.

19
nodes: 4
loaders: 7
plot types: 3
templates

Bulk RNA-seq solution 3 templates

01
Load Data
4 nodes
Load Count Matrix Load featureCounts Load Abundance (Kallisto/Salmon)Load H5AD
02
Sample Sheet & Groups
2 nodes
Merge Cell Meta Define Groups
03
QC & Filtering
2 nodes
Bulk QC Filter Low Expressed
04
Normalization
1 node
Bulk Normalize
05
Differential Expression
1 node
Differential Expression
06
Pathways & Activity
4 nodes
GSEA / ORA PROGENy Activity Hallmark Activity CollecTRI TF Activity
07
Plots
1 node
Bulk Visualization7 plots
08
Utilities & Export
4 nodescollapsed
Subset Data Obs Inspector Save H5AD Export CSV

Methylation

DNA methylation (Illumina array)

450K / EPIC / EPIC v2 IDAT files or a pre-processed beta matrix.

19
nodes: 3
loaders: 10
plot types: 4
templates

Methylation solution 4 templates

01
Load Data
3 nodes
Load IDAT Load Methyl Beta Matrix Load H5AD
02
Sample Sheet & Groups
2 nodes
Merge Cell Meta Define Groups
03
QC & Filtering
2 nodes
Methyl QC Methyl Filter
04
Normalization
1 node
Methyl Normalize
05
Differential Methylation
3 nodes
DMP Analysis Multi-Group DM (3+ groups)DMR Analysis
06
Enrichment
2 nodes
DMP Feature Enrichment Methyl GOmeth
07
Plots
2 nodes
Methyl Visualization10 plots Methyl DMR Locus Plot
08
Utilities & Export
4 nodescollapsed
Subset Data Obs Inspector Save H5AD Export CSV

ATAC-seq

ATAC-seq (chromatin accessibility)

scATAC-seq peak matrices and Cell Ranger ATAC output.

17
nodes: 4
loaders: 6
plot types: 2
templates

ATAC-seq solution 2 templates

01
Load Data
4 nodes
Load Fragments Load Peak Matrix Load ATAC MEX Load H5AD
02
QC & Peaks
2 nodes
ATAC QC Peak Calling
03
Dimensionality Reduction & Clustering
4 nodes
LSI Neighbors UMAP Clustering
04
Differential & Motifs
2 nodes
Chrom Accessibility Motif Analysis
05
Plots
1 node
ATAC Visualization6 plots
06
Utilities & Export
4 nodescollapsed
Subset Data Obs Inspector Save H5AD Export CSV

By category

The same 119 nodes, by what they do.

Categories are how the reference documentation is organised. Each card opens the full parameter tables for its nodes.

Input / Output

16 nodes

Loaders, merging, subsetting, save/export.

Load H5AD · Load 10X H5 · Load 10X MTX · Load CSV / TSV · Load Loom · Load Text · Load Velocyto Loom · Load STARsolo Velocity · Merge Data · Merge Cell Meta · Subset Data · Define Groups · Split Cell ID · Obs Inspector · Save H5AD · Export CSV

Parameter reference

Preprocessing

06 nodes

QC, normalize, log1p, HVG, scale, doublet detection.

Quality Control · Normalize · Log1p · Highly Variable Genes · Scale · Doublet Detection

Parameter reference

Analysis

08 nodes

PCA, neighbors, UMAP, t-SNE, clustering, DEG, Harmony.

PCA · Neighbors · UMAP · t-SNE · Clustering · Edit Clusters · DEG Analysis · Harmony

Parameter reference

Trajectory

08 nodes

PAGA, DPT, diffusion map, draw graph, RNA velocity.

PAGA · DPT · Diffusion Map · Draw Graph · RNA Velocity · Velocity Graph · Latent Time · Terminal States

Parameter reference

CellRank

05 nodes

Markov-chain fate analysis: kernel, fate, drivers, gene trends.

CellRank Kernel · Cell Fate Analysis · Lineage Drivers · CellRank Visualization · Gene Trends

Parameter reference

Annotation

04 nodes

LLM-based and reference-based cell type annotation.

Auto Annotation · Cell Mapper · CellTypist Annotation · Annotation Concordance

Parameter reference

Pathway

02 nodes

Top-DEG list extraction and Enrichr GO/KEGG enrichment.

Top DEG Gene List · Pathway Enrichment

Parameter reference

Functional Activity

03 nodes

Expression-based pathway and transcription-factor activity inference.

PROGENy Activity · Hallmark Activity · CollecTRI TF Activity

Parameter reference

Cell-Cell Communication

04 nodes

Ligand-receptor interaction analysis — CellPhoneDB + LIANA consensus.

CellPhoneDB · CellPhoneDB Plot · LIANA · LIANA Plot

Parameter reference

Visualization

09 nodes

Embeddings, markers, HVG, doublet, trajectory, velocity, pathway plots.

Embedding Plot · PCA Visualization · Cluster Visualization · Marker Visualization · HVG Visualization · Doublet Visualization · Trajectory Visualization · Velocity Visualization · Pathway Visualization

Parameter reference

Spatial

24 nodes

Spatial coordinates, density QC, grouping, neighbors, squidpy stats.

Load Transcripts · Add Coordinates · Spatial Density QC · Spatial Grouping · Spatial Viewer · Spatial Neighbors · Nhood Enrichment · Co-Occurrence · Spatial Autocorrelation · Load Visium (SpaceRanger) · Load Xenium · Load Visium HD · Load MERSCOPE · Load CosMx · Spatial Graph Statistics · Spot Deconvolution (NNLS) · Spatial Image Features · Spatial Hotspot · Spatial Ligand-Receptor · Spatial Domains (BANKSY) · Cellular Neighborhood · Ripley · Ligand-Receptor · Spatial Visualization

Parameter reference

Bulk RNA-seq

09 nodes

featureCounts/Salmon/Kallisto loaders, DESeq2 DE, GSEA.

Load Count Matrix · Load featureCounts · Load Abundance (Kallisto/Salmon) · Bulk QC · Bulk Normalize · Filter Low Expressed · Differential Expression · GSEA / ORA · Bulk Visualization

Parameter reference

Methylation

12 nodes

IDAT/beta loaders, DMP/DMR, directional GOmeth, cCRE/BED enrichment.

Load IDAT · Load Methyl Beta Matrix · Methyl QC · Methyl Normalize · Methyl Filter · DMP Analysis · Multi-Group DM (3+ groups) · DMR Analysis · DMP Feature Enrichment · Methyl Visualization · Methyl DMR Locus Plot · Methyl GOmeth

Parameter reference

ATAC-seq

09 nodes

Fragments/peak loaders, LSI, motif analysis.

Load ATAC MEX · Load Fragments · Load Peak Matrix · ATAC QC · Peak Calling · LSI · Chrom Accessibility · Motif Analysis · ATAC Visualization

Parameter reference

119 nodes · 14 categories · 33 templates

Start from a template, then swap any node.

Every template opens as an editable graph. The parameter reference documents each node the way the property panel shows it.

Full node reference Workflow templates