v0.4.7
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API
PyDESeq2
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PyDESeq2
Index
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Index
A
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B
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C
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D
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F
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G
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
|
X
A
alpha_mle() (DefaultInference method)
(Inference method)
alt_hypothesis (DeseqStats attribute)
B
base_mean (DeseqStats attribute)
build_design_matrix() (in module pydeseq2.utils)
C
calculate_cooks() (DeseqDataSet method)
contrast_idx (DeseqStats attribute)
contrast_vector (DeseqStats attribute)
counts_to_refit (DeseqDataSet attribute)
D
DefaultInference (class in pydeseq2.default_inference)
deseq2() (DeseqDataSet method)
deseq2_norm() (in module pydeseq2.preprocessing)
deseq2_norm_fit() (in module pydeseq2.preprocessing)
deseq2_norm_transform() (in module pydeseq2.preprocessing)
DeseqDataSet (class in pydeseq2.dds)
DeseqStats (class in pydeseq2.ds)
design_matrix (DeseqStats attribute)
disp_function() (DeseqDataSet method)
dispersion_trend() (in module pydeseq2.utils)
dispersion_trend_gamma_glm() (DefaultInference method)
(Inference method)
dnb_nll() (in module pydeseq2.utils)
F
filtered_genes (DeseqDataSet attribute)
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() (DefaultInference static method)
(in module pydeseq2.utils)
(Inference method)
fit_rough_dispersions() (DefaultInference static method)
(in module pydeseq2.utils)
(Inference method)
fit_size_factors() (DeseqDataSet method)
fit_type (DeseqDataSet attribute)
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
Inference (class in pydeseq2.inference)
irls() (DefaultInference method)
(Inference method)
irls_solver() (in module pydeseq2.utils)
L
layers (DeseqDataSet attribute)
LFC (DeseqStats attribute)
lfc_null (DeseqStats attribute)
lfc_shrink() (DeseqStats method)
lfc_shrink_nbinom_glm() (DefaultInference method)
(Inference method)
lin_reg_mu() (DefaultInference method)
(Inference method)
load_example_data() (in module pydeseq2.utils)
logmeans (DeseqDataSet attribute)
lowess() (in module pydeseq2.utils)
M
make_MA_plot() (in module pydeseq2.utils)
make_scatter() (in module pydeseq2.utils)
mean_absolute_deviation() (in module pydeseq2.utils)
module
pydeseq2.grid_search
pydeseq2.preprocessing
pydeseq2.utils
N
n_or_more_replicates() (in module pydeseq2.utils)
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)
plot_dispersions() (DeseqDataSet method)
plot_MA() (DeseqStats method)
pydeseq2.grid_search
module
pydeseq2.preprocessing
module
pydeseq2.utils
module
Q
quiet (DeseqDataSet attribute)
(DeseqStats attribute)
R
refit() (DeseqDataSet method)
replace_underscores() (in module pydeseq2.utils)
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)
vst() (DeseqDataSet method)
vst_fit() (DeseqDataSet method)
vst_transform() (DeseqDataSet method)
W
wald_test() (DefaultInference method)
(in module pydeseq2.utils)
(Inference method)
X
X (DeseqDataSet attribute)
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