PyDESeq2
v0.3
General
Installation
Requirements
Contributing
References
API
PyDESeq2
Tutorials
Getting Started
PyDESeq2
»
Index
Edit on GitHub
Index
B
|
C
|
D
|
F
|
G
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
X
B
base_mean (DeseqStats attribute)
build_design_matrix() (in module pydeseq2.utils)
C
calculate_cooks() (DeseqDataSet method)
contrast_idx (DeseqStats attribute)
counts_to_refit (DeseqDataSet attribute)
D
deseq2() (DeseqDataSet method)
deseq2_norm() (in module pydeseq2.preprocessing)
DeseqDataSet (class in pydeseq2.dds)
DeseqStats (class in pydeseq2.ds)
design_matrix (DeseqStats attribute)
dispersion_trend() (in module pydeseq2.utils)
dnb_nll() (in module pydeseq2.utils)
F
fit_alpha_mle() (in module pydeseq2.utils)
fit_dispersion_prior() (DeseqDataSet method)
fit_dispersion_trend() (DeseqDataSet method)
fit_genewise_dispersions() (DeseqDataSet method)
fit_LFC() (DeseqDataSet method)
fit_lin_mu() (in module pydeseq2.utils)
fit_MAP_dispersions() (DeseqDataSet method)
fit_moments_dispersions() (in module pydeseq2.utils)
fit_rough_dispersions() (in module pydeseq2.utils)
fit_size_factors() (DeseqDataSet method)
G
get_num_processes() (in module pydeseq2.utils)
grid_fit_alpha() (in module pydeseq2.grid_search)
grid_fit_beta() (in module pydeseq2.grid_search)
grid_fit_shrink_beta() (in module pydeseq2.grid_search)
I
irls_solver() (in module pydeseq2.utils)
L
layers (DeseqDataSet attribute)
LFC (DeseqStats attribute)
lfc_shrink() (DeseqStats method)
load_example_data() (in module pydeseq2.utils)
M
module
pydeseq2.grid_search
pydeseq2.preprocessing
pydeseq2.utils
N
n_processes (DeseqDataSet attribute)
(DeseqStats attribute)
nb_nll() (in module pydeseq2.utils)
nbinomFn() (in module pydeseq2.utils)
nbinomGLM() (in module pydeseq2.utils)
new_all_zeroes_genes (DeseqDataSet attribute)
non_zero_genes (DeseqDataSet attribute)
non_zero_idx (DeseqDataSet attribute)
O
obs (DeseqDataSet attribute)
obsm (DeseqDataSet attribute)
P
p_values (DeseqStats attribute)
padj (DeseqStats attribute)
pydeseq2.grid_search
module
pydeseq2.preprocessing
module
pydeseq2.utils
module
R
refit() (DeseqDataSet method)
results_df (DeseqStats attribute)
robust_method_of_moments_disp() (in module pydeseq2.utils)
run_wald_test() (DeseqStats method)
S
SE (DeseqStats attribute)
shrunk_LFCs (DeseqStats attribute)
statistics (DeseqStats attribute)
summary() (DeseqStats method)
T
test_valid_counts() (in module pydeseq2.utils)
trimmed_cell_variance() (in module pydeseq2.utils)
trimmed_mean() (in module pydeseq2.utils)
trimmed_variance() (in module pydeseq2.utils)
U
uns (DeseqDataSet attribute)
V
var (DeseqDataSet attribute)
varm (DeseqDataSet attribute)
vec_nb_nll() (in module pydeseq2.grid_search)
W
wald_test() (in module pydeseq2.utils)
X
X (DeseqDataSet attribute)
Read the Docs
v: v0.3
Versions
latest
stable
v0.3
v0.2.1
improve_docs_type_hinting
Downloads
On Read the Docs
Project Home
Builds