Getting started
  • Installation
Reference
  • Dashboard
    • delete workspace
    • export workspace
    • import workspace
    • new workspace
  • Upload
    • external sources
    • scanpy dataset
    • upload file
  • Preprocess
    • annotate hb
    • annotate mito
    • annotate ribo
    • batch effect removal
    • cell cycle scoring
    • downsample data
    • filter cells
    • filter genes
    • filter highest expr genes
    • filter highly variable genes
    • measure gene counts
    • normalize counts
    • pca
    • recipes
    • regress out
    • remove genes
    • run doubletdetection
    • run scrublet
    • scale to unit variance
    • subsample data
  • Integrate
    • bbknn
    • concat
    • ingest
    • quick map
    • scanorama integrate
    • scanvi integrate
    • scvi integrate
    • scvi integrate graphs
    • scvi metrics
    • umap
  • Create CiteSeq model
    • init model
  • Create Solo model
    • init model
  • Create linear vae
    • init model
  • Cluster plots
    • autoencoder cluster plot
    • neighbourhood graph
    • pca graph
    • tsne graph
    • variance ratio graph
  • Differential gene expression
    • add embeddings
    • do umap
    • rank genes groups
    • show top ranked genes
    • stat tests
    • upload marker genes
    • visualize
  • Trajectory inference
    • diffusion pseudotime
    • draw graph
    • paga clustering
  • Spatial transcriptomics
    • centrality score
    • co occurance score
    • interaction matrix
    • neighbourhood enrichment
    • ripley score
    • spatial scatter
  • Plotly 3D
    • plot chart
  • Sidebar
    • add experiment
    • download adata
    • export script
    • gene format
    • notes
    • show preview
    • species
Tutorials
  • Clustering
    • 1. Setting up workspace
    • 2. Preprocessing
    • 3. Training an autoencoder
    • 4. Cluster plots
    • 5. Differential Gene Expression
  • Trajectory Inference
  • Spatial transcriptomics
Nuwa
  • tutorials
  • README.md

Tutorials

  • Clustering
    • Setting up workspace
    • Preprocessing
    • Training an autoencoder
    • Cluster plots
    • Differential Gene Expression
  • Trajectory Inference
  • Spatial transcriptomics

2024, Nuwa Revision 25b3bfb
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This Software is under the terms of MIT License.