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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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I
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J
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K
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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
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X
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Z
_
_gene_set_coll (genometools.enrichment.GeneSetEnrichmentAnalysis attribute)
_genome (genometools.enrichment.GeneSetEnrichmentAnalysis attribute)
A
abs() (in module genometools.misc)
add() (genometools.misc.set method)
all() (in module genometools.misc)
any() (in module genometools.misc)
append() (genometools.misc.bytearray method)
apply() (in module genometools.misc)
argmax() (in module genometools.misc)
argmin() (in module genometools.misc)
argsort() (in module genometools.misc)
ArithmeticError
as_integer_ratio() (genometools.misc.float method)
ascii() (in module genometools.misc)
AssertionError
AttributeError
B
BaseException
basestring (class in genometools.misc)
bin() (in module genometools.misc)
bisect_index() (in module genometools.misc)
bit_length() (genometools.misc.long method)
bool (class in genometools.misc)
buffer (class in genometools.misc)
BufferError
bytearray (class in genometools.misc)
bytes (in module genometools.misc)
BytesWarning
C
callable() (in module genometools.misc)
capitalize() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
center() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
center_genes() (genometools.expression.ExpMatrix method)
chr() (in module genometools.misc)
chromosome (genometools.expression.ExpGene attribute)
classmethod (class in genometools.misc)
clear() (genometools.misc.set method)
close() (genometools.misc.file method)
closed (genometools.misc.file attribute)
cmp() (in module genometools.misc)
code (genometools.misc.SystemExit attribute)
coerce() (in module genometools.misc)
collection (genometools.basic.GeneSet attribute)
compile() (in module genometools.misc)
complex (class in genometools.misc)
configure_logger() (in module genometools.misc)
conjugate() (genometools.misc.complex method)
(genometools.misc.float method)
(genometools.misc.long method)
copy() (genometools.misc.frozenset method)
(genometools.misc.set method)
count() (genometools.misc.bytearray method)
(genometools.misc.tuple method)
(genometools.misc.unicode method)
D
decode() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
delattr() (in module genometools.misc)
deleter() (genometools.misc.property method)
denominator (genometools.misc.long attribute)
DeprecationWarning
description (genometools.basic.GeneSet attribute)
dict (in module genometools.misc)
difference() (genometools.misc.frozenset method)
(genometools.misc.set method)
difference_update() (genometools.misc.set method)
dir() (in module genometools.misc)
discard() (genometools.misc.set method)
divmod() (in module genometools.misc)
E
encode() (genometools.misc.unicode method)
encoding (genometools.misc.file attribute)
(genometools.misc.UnicodeDecodeError attribute)
(genometools.misc.UnicodeEncodeError attribute)
(genometools.misc.UnicodeTranslateError attribute)
end (genometools.misc.UnicodeDecodeError attribute)
(genometools.misc.UnicodeEncodeError attribute)
(genometools.misc.UnicodeTranslateError attribute)
endswith() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
ensembl_id (genometools.expression.ExpGene attribute)
enumerate (class in genometools.misc)
EnvironmentError
EOFError
errno (genometools.misc.EnvironmentError attribute)
errors (genometools.misc.file attribute)
eval() (in module genometools.misc)
Exception
execfile() (in module genometools.misc)
expandtabs() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
ExpGene (class in genometools.expression)
ExpGenome (class in genometools.expression)
ExpHeatmap (class in genometools.expression.visualize)
ExpMatrix (class in genometools.expression)
,
[1]
ExpProfile (class in genometools.expression)
extend() (genometools.misc.bytearray method)
F
file (class in genometools.misc)
filename (genometools.misc.EnvironmentError attribute)
(genometools.misc.SyntaxError attribute)
fileno() (genometools.misc.file method)
filter (in module genometools.misc)
filter_against_genome() (genometools.expression.ExpMatrix method)
(genometools.expression.ExpProfile method)
filter_variance() (in module genometools.expression)
find() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
flatten() (in module genometools.misc)
float (class in genometools.misc)
FloatingPointError
flush() (genometools.misc.file method)
fold_enrichment (genometools.enrichment.StaticGSEResult attribute)
format() (genometools.misc.unicode method)
(in module genometools.misc)
from_dict() (genometools.expression.ExpGene class method)
from_gene_names() (genometools.expression.ExpGenome class method)
from_list() (genometools.basic.GeneSet class method)
fromhex() (genometools.misc.bytearray method)
(genometools.misc.float method)
frozenset (class in genometools.misc)
ftp_download() (in module genometools.misc)
FutureWarning
G
gene (genometools.expression.visualize.HeatmapGeneAnnotation attribute)
gene_names (genometools.expression.ExpGenome attribute)
gene_set (genometools.enrichment.RankBasedGSEResult attribute)
(genometools.enrichment.StaticGSEResult attribute)
(genometools.expression.ExpGenome attribute)
gene_sets (genometools.basic.GeneSetCollection attribute)
GeneratorExit
genes (genometools.basic.GeneSet attribute)
(genometools.expression.ExpGenome attribute)
,
[1]
(genometools.expression.ExpMatrix attribute)
,
[1]
,
[2]
(genometools.expression.ExpProfile attribute)
,
[1]
GeneSet (class in genometools.basic)
GeneSetCollection (class in genometools.basic)
GeneSetEnrichmentAnalysis (class in genometools.enrichment)
genome (genometools.expression.ExpMatrix attribute)
(genometools.expression.ExpProfile attribute)
genometools.basic (module)
genometools.enrichment (module)
genometools.expression (module)
genometools.misc (module)
genometools.ontology (module)
get_by_id() (genometools.basic.GeneSetCollection method)
get_by_index() (genometools.basic.GeneSetCollection method)
get_figure() (genometools.expression.ExpMatrix method)
(genometools.expression.visualize.ExpHeatmap method)
(genometools.expression.visualize.SampleCorrelationHeatmap method)
get_file_checksum() (in module genometools.misc)
get_file_md5sum() (in module genometools.misc)
get_file_size() (in module genometools.misc)
get_fize_size() (in module genometools.misc)
get_heatmap() (genometools.expression.ExpMatrix method)
get_logger() (in module genometools.misc)
get_pretty_format() (genometools.enrichment.StaticGSEResult method)
get_rank_based_enrichment() (genometools.enrichment.GeneSetEnrichmentAnalysis method)
get_static_enrichment() (genometools.enrichment.GeneSetEnrichmentAnalysis method)
get_url_file_name() (in module genometools.misc)
get_url_size() (in module genometools.misc)
getattr() (in module genometools.misc)
getter() (genometools.misc.property method)
globals() (in module genometools.misc)
gzip_open_text() (in module genometools.misc)
H
hasattr() (in module genometools.misc)
hash (genometools.basic.GeneSet attribute)
(genometools.expression.ExpGenome attribute)
hash() (in module genometools.misc)
HeatmapBlockAnnotation (class in genometools.expression.visualize)
HeatmapGeneAnnotation (class in genometools.expression.visualize)
HeatmapSampleAnnotation (class in genometools.expression.visualize)
hex() (genometools.misc.float method)
(in module genometools.misc)
http_download() (in module genometools.misc)
I
id() (in module genometools.misc)
id_ (genometools.basic.GeneSet attribute)
imag (genometools.misc.complex attribute)
(genometools.misc.float attribute)
(genometools.misc.long attribute)
ImportError
ImportWarning
ind_genes (genometools.enrichment.RankBasedGSEResult attribute)
IndentationError
index() (genometools.basic.GeneSetCollection method)
(genometools.expression.ExpGenome method)
(genometools.misc.bytearray method)
(genometools.misc.tuple method)
(genometools.misc.unicode method)
IndexError
indices() (genometools.misc.slice method)
input() (in module genometools.misc)
insert() (genometools.misc.bytearray method)
int (in module genometools.misc)
intern() (in module genometools.misc)
intersection() (genometools.misc.frozenset method)
(genometools.misc.set method)
intersection_update() (genometools.misc.set method)
IOError
is_integer() (genometools.misc.float method)
is_writable() (in module genometools.misc)
isalnum() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
isalpha() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
isatty() (genometools.misc.file method)
isdecimal() (genometools.misc.unicode method)
isdigit() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
isdisjoint() (genometools.misc.frozenset method)
(genometools.misc.set method)
isinstance() (in module genometools.misc)
islower() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
isnumeric() (genometools.misc.unicode method)
isspace() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
issubclass() (in module genometools.misc)
issubset() (genometools.misc.frozenset method)
(genometools.misc.set method)
issuperset() (genometools.misc.frozenset method)
(genometools.misc.set method)
istitle() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
isupper() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
iter() (in module genometools.misc)
J
join() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
K
KeyboardInterrupt
KeyError
L
label (genometools.expression.ExpProfile attribute)
,
[1]
len() (in module genometools.misc)
lineno (genometools.misc.SyntaxError attribute)
list (in module genometools.misc)
ljust() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
locals() (in module genometools.misc)
long (class in genometools.misc)
LookupError
lower() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
lstrip() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
M
make_sure_dir_exists() (in module genometools.misc)
map (in module genometools.misc)
max() (in module genometools.misc)
MemoryError
memoryview (class in genometools.misc)
min() (in module genometools.misc)
mode (genometools.misc.file attribute)
msg (genometools.misc.SyntaxError attribute)
N
n (genometools.basic.GeneSetCollection attribute)
N (genometools.enrichment.StaticGSEResult attribute)
n (genometools.enrichment.StaticGSEResult attribute)
(genometools.expression.ExpMatrix attribute)
name (genometools.basic.GeneSet attribute)
(genometools.expression.ExpGene attribute)
(genometools.misc.file attribute)
NameError
newlines (genometools.misc.file attribute)
next (genometools.misc.enumerate attribute)
(genometools.misc.file attribute)
(genometools.misc.reversed attribute)
next() (in module genometools.misc)
NotImplementedError
numerator (genometools.misc.long attribute)
O
object (genometools.misc.UnicodeDecodeError attribute)
(genometools.misc.UnicodeEncodeError attribute)
(genometools.misc.UnicodeTranslateError attribute)
(in module genometools.misc)
oct() (in module genometools.misc)
offset (genometools.misc.SyntaxError attribute)
open() (in module genometools.misc)
ord() (in module genometools.misc)
OSError
OverflowError
P
p (genometools.expression.ExpMatrix attribute)
(genometools.expression.ExpProfile attribute)
partition() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
PendingDeprecationWarning
pop() (genometools.misc.bytearray method)
(genometools.misc.set method)
position (genometools.expression.ExpGene attribute)
pow() (in module genometools.misc)
print() (in module genometools.misc)
print_file_and_line (genometools.misc.SyntaxError attribute)
property (class in genometools.misc)
pval (genometools.enrichment.StaticGSEResult attribute)
Q
quantile_normalize() (in module genometools.expression)
R
range (in module genometools.misc)
RankBasedGSEResult (class in genometools.enrichment)
raw_input() (in module genometools.misc)
read() (genometools.misc.file method)
read_all() (in module genometools.misc)
read_msigdb_xml() (genometools.basic.GeneSetCollection class method)
read_single() (in module genometools.misc)
read_tsv() (genometools.basic.GeneSetCollection class method)
(genometools.expression.ExpGenome class method)
(genometools.expression.ExpMatrix class method)
(genometools.expression.ExpProfile class method)
readinto() (genometools.misc.file method)
readline() (genometools.misc.file method)
readlines() (genometools.misc.file method)
real (genometools.misc.complex attribute)
(genometools.misc.float attribute)
(genometools.misc.long attribute)
reason (genometools.misc.UnicodeDecodeError attribute)
(genometools.misc.UnicodeEncodeError attribute)
(genometools.misc.UnicodeTranslateError attribute)
reduce() (in module genometools.misc)
ReferenceError
reload() (in module genometools.misc)
remove() (genometools.misc.bytearray method)
(genometools.misc.set method)
replace() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
repr() (in module genometools.misc)
reverse() (genometools.misc.bytearray method)
reversed (class in genometools.misc)
rfind() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
rindex() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
rjust() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
round() (in module genometools.misc)
rpartition() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
rsplit() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
rstrip() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
RuntimeError
RuntimeWarning
S
sample (genometools.expression.visualize.HeatmapSampleAnnotation attribute)
sample_correlations (genometools.expression.ExpMatrix attribute)
SampleCorrelationHeatmap (class in genometools.expression.visualize)
samples (genometools.expression.ExpMatrix attribute)
,
[1]
,
[2]
seek() (genometools.misc.file method)
selected_genes (genometools.enrichment.StaticGSEResult attribute)
set (class in genometools.misc)
setattr() (in module genometools.misc)
setter() (genometools.misc.property method)
size (genometools.basic.GeneSet attribute)
slice (class in genometools.misc)
smart_open_read() (in module genometools.misc)
smart_open_write() (in module genometools.misc)
softspace (genometools.misc.file attribute)
sort_genes() (genometools.expression.ExpMatrix method)
(genometools.expression.ExpProfile method)
sort_samples() (genometools.expression.ExpMatrix method)
sorted() (in module genometools.misc)
source (genometools.basic.GeneSet attribute)
split() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
splitlines() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
StandardError
standardize_genes() (genometools.expression.ExpMatrix method)
start (genometools.misc.UnicodeDecodeError attribute)
(genometools.misc.UnicodeEncodeError attribute)
(genometools.misc.UnicodeTranslateError attribute)
startswith() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
StaticGSEResult (class in genometools.enrichment)
staticmethod (class in genometools.misc)
StopIteration
str (in module genometools.misc)
strerror (genometools.misc.EnvironmentError attribute)
strip() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
sum() (in module genometools.misc)
super() (in module genometools.misc)
swapcase() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
symmetric_difference() (genometools.misc.frozenset method)
(genometools.misc.set method)
symmetric_difference_update() (genometools.misc.set method)
SyntaxError
SyntaxWarning
SystemError
SystemExit
T
TabError
tell() (genometools.misc.file method)
test_dir_writable() (in module genometools.misc)
test_file_checksum() (in module genometools.misc)
test_file_writable() (in module genometools.misc)
text (genometools.misc.SyntaxError attribute)
title() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
to_list() (genometools.basic.GeneSet method)
translate() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
truncate() (genometools.misc.file method)
tuple (class in genometools.misc)
TypeError
U
UnboundLocalError
unichr() (in module genometools.misc)
unicode (class in genometools.misc)
UnicodeDecodeError
UnicodeEncodeError
UnicodeError
UnicodeTranslateError
UnicodeWarning
union() (genometools.misc.frozenset method)
(genometools.misc.set method)
update() (genometools.misc.set method)
upper() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
UserWarning
V
ValueError
vars() (in module genometools.misc)
W
Warning
write() (genometools.misc.file method)
write_tsv() (genometools.basic.GeneSetCollection method)
(genometools.expression.ExpGenome method)
(genometools.expression.ExpMatrix method)
(genometools.expression.ExpProfile method)
writelines() (genometools.misc.file method)
X
X (genometools.expression.ExpMatrix attribute)
,
[1]
,
[2]
x (genometools.expression.ExpProfile attribute)
,
[1]
xrange (class in genometools.misc)
xreadlines() (genometools.misc.file method)
Z
ZeroDivisionError
zfill() (genometools.misc.bytearray method)
(genometools.misc.unicode method)
zip (in module genometools.misc)
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