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API
Preprocessing:
Methods:
Running multiple methods:
General utils:
AnnData utils:
Omnipath wrappers:
Plotting
Metrics
Benchmark utils
Benchmark
decoupler.benchmark
decoupler.format_benchmark_inputs
format_benchmark_inputs()
decoupler.get_performances
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Release notes
Reference
Vignettes
Usage
Cell type annotation from marker genes
Pathway activity inference
Transcription factor activity inference
Functional enrichment of biological terms
Pseudo-bulk functional analysis
Spatial functional analysis
Bulk functional analysis
Benchmarking pipeline
Conversion to other organisms
decoupler
API
decoupler.format_benchmark_inputs
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decoupler.format_benchmark_inputs
decoupler.
format_benchmark_inputs
(
mat
,
obs
,
perturb
,
sign
,
net
,
groupby
,
by
,
f_expr
=
True
,
f_srcs
=
False
,
source
=
'source'
,
target
=
'target'
,
weight
=
'weight'
,
min_n
=
5
,
verbose
=
False
,
use_raw
=
True
,
decouple_kws
=
{}
)
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