kMer
Introduction
Installation
Dependencies
Latest kMer release
kMer development version
Methodology
k
-mer counting
Distance metrics
Strand balance
Profile shrinking
Scaling and smoothing
Tutorial
k
-mer counting
Merging profiles
Distance between profiles
Enforcing strand balance
Custom merge functions
Using the Python library
k
-mer profiles
Storing
k
-mer profiles
Differences between
k
-mer profiles
API reference
k
-mer profiles
k
-mer profile distances
Metrics
Development
Contributing
Documentation
Unit tests
Coding style
Versioning
Release procedure
k
-mer profile file format
Versioning
Current version: 1.0.0
Changes from older versions
Changelog
Version 1.0.1
Version 1.0.0
Support Python 3.3 and 3.4
Generalize custom function arguments
Version 0.3.0
Version 0.2.0
Version 0.1.0
Copyright
Authors
License
kMer
Docs
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Edit on GitHub
Index
B
|
C
|
D
|
E
|
F
|
G
|
K
|
M
|
N
|
P
|
R
|
S
|
T
|
V
B
balance() (k_mer.klib.Profile method)
binary_to_dna() (k_mer.klib.Profile method)
C
copy() (k_mer.klib.Profile method)
cosine_similarity() (in module k_mer.metrics)
D
distance() (k_mer.kdistlib.ProfileDistance method)
distance_matrix() (in module k_mer.kdistlib)
distribution() (in module k_mer.metrics)
dna_to_binary() (k_mer.klib.Profile method)
dynamic_smooth() (k_mer.kdistlib.ProfileDistance method)
E
euclidean() (in module k_mer.metrics)
F
from_fasta() (k_mer.klib.Profile class method)
from_file() (k_mer.klib.Profile class method)
from_file_old_format() (k_mer.klib.Profile class method)
G
get_scale() (in module k_mer.metrics)
K
k_mer.kdistlib (module)
k_mer.klib (module)
k_mer.metrics (module)
M
mean (k_mer.klib.Profile attribute)
median (k_mer.klib.Profile attribute)
merge() (k_mer.klib.Profile method)
mergers (in module k_mer.metrics)
multiset() (in module k_mer.metrics)
N
non_zero (k_mer.klib.Profile attribute)
number (k_mer.klib.Profile attribute)
P
pairwise (in module k_mer.metrics)
positive() (in module k_mer.metrics)
print_counts() (k_mer.klib.Profile method)
Profile (class in k_mer.klib)
ProfileDistance (class in k_mer.kdistlib)
R
reverse_complement() (k_mer.klib.Profile method)
S
save() (k_mer.klib.Profile method)
scale_down() (in module k_mer.metrics)
shrink() (k_mer.klib.Profile method)
shuffle() (k_mer.klib.Profile method)
split() (k_mer.klib.Profile method)
std (k_mer.klib.Profile attribute)
summary (in module k_mer.metrics)
T
total (k_mer.klib.Profile attribute)
V
vector_distance (in module k_mer.metrics)
vector_length() (in module k_mer.metrics)
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