GSEApy
latest
Table of Contents
1. Welcome to GSEAPY’s documentation!
2. GSEAPY Example
3. GSVA example
4. scRNA-seq Example
5. A Protocol to Prepare files for GSEApy
6. Developmental Guide
7. Frequently Asked Questions
GSEApy
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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E
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F
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G
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H
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L
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M
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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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W
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Z
A
add_filter() (gseapy.biomart.Biomart method)
apply() (gseapy.base.GMT method)
B
barplot() (in module gseapy.plot)
Biomart (class in gseapy.biomart)
C
calc_metric() (gseapy.gsea.GSEA method)
calc_pvalues() (in module gseapy.stats)
check_genes() (gseapy.enrichr.Enrichr method)
D
dotplot() (in module gseapy.plot)
download_library() (in module gseapy.parser)
E
enrich() (gseapy.enrichr.Enrichr method)
(in module gseapy)
enrichment_map() (in module gseapy.plot)
enrichment_score() (gseapy.base.GSEAbase method)
Enrichr (class in gseapy.enrichr)
enrichr() (in module gseapy)
F
fdrcorrection() (in module gseapy.stats)
filter_gmt() (gseapy.enrichr.Enrichr method)
G
get_attributes() (gseapy.biomart.Biomart method)
get_background() (gseapy.enrichr.Enrichr method)
get_datasets() (gseapy.biomart.Biomart method)
get_filters() (gseapy.biomart.Biomart method)
get_libraries() (gseapy.base.GSEAbase method)
(gseapy.enrichr.Enrichr method)
get_library() (in module gseapy.parser)
get_library_name() (in module gseapy.parser)
get_marts() (gseapy.biomart.Biomart method)
get_results() (gseapy.enrichr.Enrichr method)
GMT (class in gseapy.base)
GSEA (class in gseapy.gsea)
gsea() (in module gseapy)
gsea_cls_parser() (in module gseapy.parser)
gsea_edb_parser() (gseapy.gsea.Replot method)
(in module gseapy.parser)
GSEAbase (class in gseapy.base)
gseaplot() (in module gseapy.plot)
gseaplot2() (in module gseapy.plot)
gseapy
module
gseapy.base
module
gseapy.biomart
module
gseapy.enrichr
module
gseapy.gsea
module
gseapy.parser
module
gseapy.plot
module
gseapy.scipalette
module
gseapy.stats
module
H
heatmap() (in module gseapy.plot)
L
load_classes() (gseapy.gsea.GSEA method)
load_data() (gseapy.gsea.GSEA method)
load_gmt() (gseapy.base.GSEAbase method)
load_gmt_only() (gseapy.base.GSEAbase method)
M
MidpointNormalize (class in gseapy.plot)
module
gseapy
gseapy.base
gseapy.biomart
gseapy.enrichr
gseapy.gsea
gseapy.parser
gseapy.plot
gseapy.scipalette
gseapy.stats
multiple_testing_correction() (in module gseapy.stats)
P
parse_background() (gseapy.enrichr.Enrichr method)
parse_genelists() (gseapy.enrichr.Enrichr method)
parse_genesets() (gseapy.enrichr.Enrichr method)
parse_gmt() (gseapy.base.GSEAbase method)
plot() (gseapy.base.GSEAbase method)
prepare_outdir() (gseapy.base.GSEAbase method)
(gseapy.enrichr.Enrichr method)
Prerank (class in gseapy.gsea)
prerank() (in module gseapy)
Q
query() (gseapy.biomart.Biomart method)
query_simple() (gseapy.biomart.Biomart method)
R
read_gmt() (in module gseapy.parser)
Replot (class in gseapy.gsea)
replot() (in module gseapy)
results (gseapy.base.GSEAbase property)
ringplot() (in module gseapy.plot)
run() (gseapy.enrichr.Enrichr method)
(gseapy.gsea.GSEA method)
(gseapy.gsea.Prerank method)
(gseapy.gsea.Replot method)
S
send_genes() (gseapy.enrichr.Enrichr method)
set_organism() (gseapy.enrichr.Enrichr method)
ssgsea() (in module gseapy)
T
to_df() (gseapy.base.GSEAbase method)
W
write() (gseapy.base.GMT method)
Z
zscore() (in module gseapy.plot)
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