pygenesig
latest
User's Guide
Pygenesig, a framework to generate and validate tissue-specific gene signatures.
Prepare data
Creating signatures
Testing signatures
Putting it together: crossvalidation
Case studies
Developer's Guide
Implement own methods
API documentation
pygenesig
core
File input/output (
pygenesig.file_formats
)
Signature Generators
Signature Testers
Auxilary functions (
pygenesig.tools
)
pygenesig
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Index
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Index
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C
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J
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_
_mk_signatures() (pygenesig.validation.SignatureGenerator method)
_score_signatures() (pygenesig.validation.SignatureTester method)
C
classify() (pygenesig.validation.SignatureTester method)
collapse_matrix() (in module pygenesig.tools)
combine_signatures() (in module pygenesig.tools)
confusion_matrix() (pygenesig.validation.SignatureTester method)
cv_score() (in module pygenesig.validation)
F
f1_neg() (in module pygenesig.perfmeasures)
f1_pos() (in module pygenesig.perfmeasures)
filter_samples() (in module pygenesig.validation)
fold_change() (in module pygenesig.mcp_counter)
G
get_gini_signatures() (in module pygenesig.gini)
get_rogini_format() (in module pygenesig.gini)
(pygenesig.gini.GiniSignatureGenerator method)
gini() (in module pygenesig.gini)
GiniSignatureGenerator (class in pygenesig.gini)
J
jaccard_ind() (in module pygenesig.tools)
jaccard_mat() (in module pygenesig.tools)
L
load_gmt() (in module pygenesig.file_formats)
M
make_rosetta_dict() (in module pygenesig.file_formats)
mcc() (in module pygenesig.perfmeasures)
MCPSignatureGenerator (class in pygenesig.mcp_counter)
MCPSignatureTester (class in pygenesig.mcp_counter)
mk_signatures() (pygenesig.validation.SignatureGenerator method)
module
pygenesig.file_formats
pygenesig.gini
pygenesig.mcp_counter
pygenesig.perfmeasures
pygenesig.tools
pygenesig.validation
N
normalize() (in module pygenesig.tools)
normalize_sum() (in module pygenesig.tools)
P
pairwise_jaccard_ind() (in module pygenesig.tools)
performance_per_tissue() (in module pygenesig.tools)
prec_neg() (in module pygenesig.perfmeasures)
prec_pos() (in module pygenesig.perfmeasures)
pygenesig.file_formats
module
pygenesig.gini
module
pygenesig.mcp_counter
module
pygenesig.perfmeasures
module
pygenesig.tools
module
pygenesig.validation
module
R
read_expr() (in module pygenesig.file_formats)
read_gct() (in module pygenesig.file_formats)
read_gmt() (in module pygenesig.file_formats)
read_rosetta() (in module pygenesig.file_formats)
read_target() (in module pygenesig.file_formats)
recall_neg() (in module pygenesig.perfmeasures)
recall_pos() (in module pygenesig.perfmeasures)
roc_auc() (in module pygenesig.mcp_counter)
S
score_signatures() (pygenesig.validation.SignatureTester method)
sens() (in module pygenesig.perfmeasures)
SignatureGenerator (class in pygenesig.validation)
SignatureTester (class in pygenesig.validation)
SignatureTesterException
sort_signatures() (pygenesig.validation.SignatureTester static method)
spec() (in module pygenesig.perfmeasures)
specific_fold_change() (in module pygenesig.mcp_counter)
T
translate_signatures() (in module pygenesig.tools)
W
write_expr() (in module pygenesig.file_formats)
write_gct() (in module pygenesig.file_formats)
write_gmt() (in module pygenesig.file_formats)
write_rosetta() (in module pygenesig.file_formats)
write_target() (in module pygenesig.file_formats)
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