v0.1.1
Getting Started
Installation Guide
Quickstart Guide
Tutorial
The PyCytoData Object
File IO and Datasets
CyTOF Data Preprocessing
Dimension Reuction with CytofDR
Development
Integration with PyCytoData
Contribution Guideline
Building and Testing
Development and Roadmap
Changelog
Releases
Recent Changes
License
Full API Reference
API Reference
Module: PyCytoData.data
Module: PyCytoData.preprocess
Module: PyCytoData.exceptions
Resources
References
Our Paper (Cytomulate)
CyTOF DR Review (CytofDR)
Dr. Xinlei (Shery) Wang
Dr. Tao Wang
DBAI
GitHub
PyCytoData
Index
Edit on GitHub
Index
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A
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B
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C
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D
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E
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F
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G
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L
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M
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N
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P
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R
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S
_
__add__() (PyCytoData.data.PyCytoData method)
__getitem__() (PyCytoData.data.PyCytoData method)
__iadd__() (PyCytoData.data.PyCytoData method)
__len__() (PyCytoData.data.PyCytoData method)
__str__() (PyCytoData.data.PyCytoData method)
A
add_sample() (PyCytoData.data.PyCytoData method)
arcsinh() (in module PyCytoData.preprocess)
AutoChannelError
B
bead_normalization() (in module PyCytoData.preprocess)
C
cell_types (PyCytoData.data.PyCytoData property)
channels (PyCytoData.data.PyCytoData property)
D
DataLoader (class in PyCytoData.data)
DimensionMismatchError
E
expression_matrix (PyCytoData.data.PyCytoData property)
ExpressionMatrixDimensionError
F
FileIO (class in PyCytoData.data)
G
gate_center_offset_residual() (in module PyCytoData.preprocess)
gate_debris_removal() (in module PyCytoData.preprocess)
gate_intact_cells() (in module PyCytoData.preprocess)
gate_live_cells() (in module PyCytoData.preprocess)
get_channel_expressions() (PyCytoData.data.PyCytoData method)
L
lineage_channels (PyCytoData.data.PyCytoData property)
load_dataset() (PyCytoData.data.DataLoader class method)
load_delim() (PyCytoData.data.FileIO static method)
load_expression() (PyCytoData.data.FileIO static method)
M
module
PyCytoData.exceptions
PyCytoData.preprocess
N
n_cell_types (PyCytoData.data.PyCytoData property)
n_cells (PyCytoData.data.PyCytoData property)
n_channels (PyCytoData.data.PyCytoData property)
n_samples (PyCytoData.data.PyCytoData property)
P
preprocess() (PyCytoData.data.PyCytoData method)
PyCytoData (class in PyCytoData.data)
PyCytoData.exceptions
module
PyCytoData.preprocess
module
R
reductions (PyCytoData.data.PyCytoData property)
run_dr_methods() (PyCytoData.data.PyCytoData method)
S
sample_index (PyCytoData.data.PyCytoData property)
save_2d_list_to_csv() (PyCytoData.data.FileIO static method)
save_np_array() (PyCytoData.data.FileIO static method)
subset() (PyCytoData.data.PyCytoData method)
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