MUFFIN
latest
How to use MUFFIN
Installation
Install optional R dependencies
Loading your data
Setting normalization factors
Removing unused variables
Count Modelling and transformation
Feature Selection
Dimensionnality reduction
Downstream analyses
Examples
Starter : Clustering of 3k PBMCs sequenced by 10X scRNA-seq
Paper example : 10k PBMCs sequenced by 10X scATAC-seq
Paper example : H3K4Me3 occupancy in immune cells via ChIP-seq
Paper example : Landscape of open chromatin in cancers via ATAC-seq (TCGA)
Paper example : Clustering of 10k PBMCs sequenced by 10X scRNA-seq
API reference
muffin.load
muffin.tools
muffin.great
muffin.peakMerge
muffin.plots
MUFFIN
Index
Edit on GitHub
Index
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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L
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M
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P
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R
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S
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T
B
barplot_enrich() (muffin.great.pyGREAT method)
C
cca() (in module muffin.tools)
cluster_rows_leiden() (in module muffin.tools)
cluster_treemap() (muffin.great.pyGREAT method)
compute_pa_pca() (in module muffin.tools)
compute_residuals() (in module muffin.tools)
compute_size_factors() (in module muffin.tools)
compute_umap() (in module muffin.tools)
D
dataset_from_arrays() (in module muffin.load)
dataset_from_bam() (in module muffin.load)
differential_expression_A_vs_B() (in module muffin.tools)
F
feature_selection_chisquare() (in module muffin.tools)
feature_selection_elbow() (in module muffin.tools)
feature_selection_top_k() (in module muffin.tools)
find_enriched() (muffin.great.pyGREAT method)
find_enriched_genes() (muffin.great.pyGREAT method)
find_genes_for_geneset() (muffin.great.pyGREAT method)
G
gene_activity_matrix() (muffin.great.pyGREAT method)
get_nearest_gene() (muffin.great.pyGREAT method)
L
label_by_nearest_gene() (muffin.great.pyGREAT method)
M
mega_heatmap() (in module muffin.plots)
merge_peaks() (in module muffin.peakMerge)
module
muffin.great
muffin.load
muffin.peakMerge
muffin.plots
muffin.tools
muffin.great
module
muffin.load
module
muffin.peakMerge
module
muffin.plots
module
muffin.tools
module
P
plot_reduced_dim() (in module muffin.plots)
pseudo_peak_calling() (in module muffin.tools)
pyGREAT (class in muffin.great)
R
rescale_input_center_scale() (in module muffin.tools)
rescale_input_quantile() (in module muffin.tools)
S
set_design_matrix() (in module muffin.load)
set_normalization_factors() (in module muffin.load)
set_size_factors() (in module muffin.load)
T
transfer_categorical_labels() (in module muffin.tools)
trim_low_counts() (in module muffin.tools)
tss_activity_matrix() (muffin.great.pyGREAT method)
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