HumanCellAtlas-Scanpy-CellBrowser


StepAnnotation
Step 1: Human Cell Atlas Matrix Downloader
Single cell transcriptome analysis of human pancreas
Matrix Market
Step 2: Scanpy Read10x
Output dataset 'matrix_mtx' from step 1
Output dataset 'genes_tsv' from step 1
Output dataset 'barcode_tsv' from step 1
AnnData format hdf5
Gene ID
Step 3: Scanpy FilterCells
Output dataset 'output_h5' from step 2
AnnData format hdf5
AnnData format hdf5
Parameters used to filter cells
Parameters used to filter cells 1
n_genes
0.0
1000000000.0
select at runtime
Step 4: Scanpy FilterGenes
Output dataset 'output_h5' from step 3
AnnData format hdf5
AnnData format hdf5
Parameters used to filter genes
Parameters used to filter genes 1
n_cells
0.0
1000000000.0
select at runtime
False
Step 5: Scanpy NormaliseData
Output dataset 'output_h5' from step 4
AnnData format hdf5
AnnData format hdf5
10000.0
True
False
Step 6: Scanpy FindVariableGenes
Output dataset 'output_h5' from step 5
AnnData format hdf5
AnnData format hdf5
Seurat
Parameters used to find variable genes
Parameters used to find variable genes 1
Mean of expression
0.0
1000000000.0
20
Not available.
Step 7: Scanpy ScaleData
Output dataset 'output_h5' from step 6
AnnData format hdf5
AnnData format hdf5
True
True
Empty.
Not available.
Step 8: Scanpy RunPCA
Output dataset 'output_h5' from step 7
AnnData format hdf5
AnnData format hdf5
50
False
True
Nothing selected.
0
Nothing selected.
False
Step 9: Scanpy ComputeGraph
Output dataset 'output_h5' from step 8
AnnData format hdf5
AnnData format hdf5
True
Step 10: Scanpy FindCluster
Output dataset 'output_h5' from step 9
AnnData format hdf5
AnnData format hdf5
True
True
Step 11: Scanpy RunTSNE
Output dataset 'output_h5' from step 10
AnnData format hdf5
AnnData format hdf5
True
True
False
Step 12: Scanpy FindMarkers
Output dataset 'output_h5' from step 11
AnnData format hdf5
AnnData format hdf5
50
True
True
Step 13: Scanpy RunUMAP
Output dataset 'output_h5' from step 12
AnnData format hdf5
AnnData format hdf5
True
True
False
Step 14: UCSC Cell Browser
Scanpy AnnData HDF5 serialized object
Output dataset 'output_h5' from step 13