repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
scikit-bio | skbio/tests/test_config.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 88 | 3,045 |
scikit-bio | skbio/tests/test_workflow.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 405 | 13,167 |
scikit-bio | skbio/tests/test_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 56 | 1,553 |
scikit-bio | skbio/sequence/distance.py | .py | """Sequence distance metrics (:mod:`skbio.sequence.distance`)
==========================================================
.. currentmodule:: skbio.sequence.distance
This module provides functions for computing distances between biological sequences.
These functions can be used directly on two :class:`~skbio.sequence.S... | 1,851 | 61,914 |
scikit-bio | skbio/sequence/_grammared_sequence.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 975 | 28,872 |
scikit-bio | skbio/sequence/_alphabet.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 283 | 8,775 |
scikit-bio | skbio/sequence/__init__.py | .py | r"""Biological Sequences (:mod:`skbio.sequence`)
============================================
.. currentmodule:: skbio.sequence
This module provides functionality for storing and working with sequences, including
molecular sequences based on IUPAC-defined alphabets (:class:`DNA`, :class:`RNA`,
:class:`Protein`), sequ... | 594 | 17,774 |
scikit-bio | skbio/sequence/_rna.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 476 | 14,290 |
scikit-bio | skbio/sequence/transition.py | .py | r"""Transition probability models (:mod:`skbio.sequence.tpm`)
==========================================================
.. currentmodule:: skbio.sequence.transition
This module provides functions for calculating transition probability
matrices (TPMs) under several substitution models for a specified
evolutionary dis... | 693 | 20,733 |
scikit-bio | skbio/sequence/_repr.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 112 | 4,258 |
scikit-bio | skbio/sequence/_sequence.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 2,415 | 79,738 |
scikit-bio | skbio/sequence/_dna.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 498 | 14,667 |
scikit-bio | skbio/sequence/_substitution.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 733 | 30,824 |
scikit-bio | skbio/sequence/_genetic_code.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 863 | 30,993 |
scikit-bio | skbio/sequence/_protein.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 302 | 9,721 |
scikit-bio | skbio/sequence/_nucleotide_mixin.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 377 | 10,986 |
scikit-bio | skbio/sequence/tests/test_genetic_code.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 504 | 19,666 |
scikit-bio | skbio/sequence/tests/test_alphabet.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 266 | 11,057 |
scikit-bio | skbio/sequence/tests/test_nucleotide_sequences.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 519 | 21,247 |
scikit-bio | skbio/sequence/tests/test_sequence.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 2,868 | 115,007 |
scikit-bio | skbio/sequence/tests/test_protein.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 140 | 5,067 |
scikit-bio | skbio/sequence/tests/test_dna.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 50 | 1,817 |
scikit-bio | skbio/sequence/tests/test_substitution.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 209 | 8,362 |
scikit-bio | skbio/sequence/tests/test_grammared_sequence.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 774 | 30,398 |
scikit-bio | skbio/sequence/tests/test_distance.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,091 | 37,000 |
scikit-bio | skbio/sequence/tests/test_transition.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 490 | 16,693 |
scikit-bio | skbio/sequence/tests/test_rna.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 50 | 1,913 |
scikit-bio | skbio/tree/_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 91 | 2,996 |
scikit-bio | skbio/tree/__init__.py | .py | r"""Trees and Phylogenetics (:mod:`skbio.tree`)
===========================================
.. currentmodule:: skbio.tree
This module provides functionality for working with trees, including phylogenetic trees
and various types of hierarchies with relevance in biology or beyond. It supports trees
that are multifurcat... | 630 | 19,655 |
scikit-bio | skbio/tree/_exception.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 38 | 758 |
scikit-bio | skbio/tree/_nj.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 347 | 12,483 |
scikit-bio | skbio/tree/_tree.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 6,446 | 221,965 |
scikit-bio | skbio/tree/_majority_rule.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 289 | 10,369 |
scikit-bio | skbio/tree/_upgma.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 100 | 3,081 |
scikit-bio | skbio/tree/_me.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,734 | 61,848 |
scikit-bio | skbio/tree/_compare.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 549 | 18,092 |
scikit-bio | skbio/tree/tests/test_me.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 2,090 | 86,880 |
scikit-bio | skbio/tree/tests/test_tree.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 3,383 | 128,482 |
scikit-bio | skbio/tree/tests/test_nj.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 195 | 8,260 |
scikit-bio | skbio/tree/tests/test_majority_rule.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 198 | 7,394 |
scikit-bio | skbio/tree/tests/test_upgma.py | .py | import io
from unittest import TestCase, main
from skbio import DistanceMatrix, TreeNode
from skbio.util import get_data_path
from skbio.tree._upgma import upgma
class UpgmaTests(TestCase):
def setUp(self):
data = [[0, 5, 9, 9, 8],
[5, 0, 10, 10, 9],
[9, 10, 0, 8,... | 57 | 2,099 |
scikit-bio | skbio/tree/tests/test_compare.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 224 | 7,873 |
scikit-bio | skbio/tree/tests/test_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 85 | 3,327 |
scikit-bio | skbio/diversity/_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 186 | 5,919 |
scikit-bio | skbio/diversity/_block.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 357 | 11,279 |
scikit-bio | skbio/diversity/__init__.py | .py | r"""Community Diversity (:mod:`skbio.diversity`)
============================================
.. currentmodule:: skbio.diversity
This module provides functionality for analyzing biodiversity of communities -- groups
of organisms living in the same area. It implements various metrics of **alpha**
(*within*-community) ... | 474 | 18,454 |
scikit-bio | skbio/diversity/_driver.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 461 | 16,590 |
scikit-bio | skbio/diversity/alpha/_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,561 | 41,081 |
scikit-bio | skbio/diversity/alpha/_lladser.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 622 | 18,293 |
scikit-bio | skbio/diversity/alpha/__init__.py | .py | r"""Alpha diversity measures (:mod:`skbio.diversity.alpha`)
=======================================================
.. currentmodule:: skbio.diversity.alpha
This package provides implementations of various alpha diversity [1]_ metrics,
including measures of richness, diversity, evenness, dominance, and coverage.
Som... | 229 | 4,804 |
scikit-bio | skbio/diversity/alpha/_pd.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 447 | 17,227 |
scikit-bio | skbio/diversity/alpha/_ace.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 140 | 4,567 |
scikit-bio | skbio/diversity/alpha/_chao1.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 221 | 6,370 |
scikit-bio | skbio/diversity/alpha/_gini.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 124 | 3,614 |
scikit-bio | skbio/diversity/alpha/tests/test_pd.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 404 | 16,355 |
scikit-bio | skbio/diversity/alpha/tests/test_ace.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 41 | 1,496 |
scikit-bio | skbio/diversity/alpha/tests/test_gini.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 67 | 2,304 |
scikit-bio | skbio/diversity/alpha/tests/test_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 463 | 17,564 |
scikit-bio | skbio/diversity/alpha/tests/test_chao1.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 83 | 2,937 |
scikit-bio | skbio/diversity/alpha/tests/test_lladser.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 236 | 8,608 |
scikit-bio | skbio/diversity/beta/__init__.py | .py | """Beta diversity measures (:mod:`skbio.diversity.beta`)
=====================================================
.. currentmodule:: skbio.diversity.beta
This package provides implementations of beta diversity measures for computing sample
dissimilarity. Users should also explore SciPy's :func:`~scipy.spatial.distance.p... | 34 | 1,122 |
scikit-bio | skbio/diversity/beta/_unifrac.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 620 | 23,149 |
scikit-bio | skbio/diversity/beta/tests/test_unifrac.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 692 | 29,934 |
scikit-bio | skbio/diversity/tests/test_driver.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 956 | 43,171 |
scikit-bio | skbio/diversity/tests/test_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 172 | 6,582 |
scikit-bio | skbio/diversity/tests/test_block.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 208 | 8,333 |
scikit-bio | skbio/util/_testing.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 793 | 25,381 |
scikit-bio | skbio/util/_warning.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 137 | 4,194 |
scikit-bio | skbio/util/_gpu.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 32 | 803 |
scikit-bio | skbio/util/_plotting.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 69 | 2,018 |
scikit-bio | skbio/util/__init__.py | .py | r"""Utilities for Developers (:mod:`skbio.util`)
============================================
.. currentmodule:: skbio.util
This package provides general exception/warning definitions used throughout
scikit-bio, as well as various utility functionality, including I/O and
unit-testing convenience functions.
Testing ... | 139 | 2,872 |
scikit-bio | skbio/util/_random.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 119 | 4,041 |
scikit-bio | skbio/util/_typing.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 208 | 8,378 |
scikit-bio | skbio/util/_exception.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 22 | 660 |
scikit-bio | skbio/util/_docstring.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 288 | 8,568 |
scikit-bio | skbio/util/_optionals.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 56 | 1,453 |
scikit-bio | skbio/util/_decorator.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 311 | 8,913 |
scikit-bio | skbio/util/_array.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 271 | 8,601 |
scikit-bio | skbio/util/_misc.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 210 | 5,491 |
scikit-bio | skbio/util/tests/test_optionals.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 61 | 2,002 |
scikit-bio | skbio/util/tests/test_warning.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 109 | 3,837 |
scikit-bio | skbio/util/tests/test_misc.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 249 | 7,854 |
scikit-bio | skbio/util/tests/test_testing.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 934 | 36,262 |
scikit-bio | skbio/util/tests/test_docstring.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 379 | 12,257 |
scikit-bio | skbio/util/tests/test_array.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 468 | 16,916 |
scikit-bio | skbio/util/tests/test_plotting.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 81 | 2,284 |
scikit-bio | skbio/util/tests/test_decorator.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 270 | 7,213 |
scikit-bio | skbio/util/tests/test_random.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 97 | 3,289 |
scikit-bio | skbio/stats/_subsample.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 253 | 7,968 |
scikit-bio | skbio/stats/__init__.py | .py | r"""Multivariate Statistics (:mod:`skbio.stats`)
============================================
.. currentmodule:: skbio.stats
This module provides various statistical methods to support the analyses of
high-dimensional biological data to uncover the relationships among samples,
features and metadata. Examples include ... | 72 | 1,465 |
scikit-bio | skbio/stats/power.py | .py | r"""Empirical Power Estimation (:mod:`skbio.stats.power`)
=====================================================
.. currentmodule:: skbio.stats.power
The purpose of this module is to provide empirical, post-hoc power estimation
of normally and non-normally distributed data. It also provides support to
subsample data t... | 1,231 | 47,548 |
scikit-bio | skbio/stats/gradient.py | .py | r"""Gradient analyses (:mod:`skbio.stats.gradient`)
===============================================
.. currentmodule:: skbio.stats.gradient
This module provides functionality for performing gradient analyses.
The algorithms included in this module mainly allows performing analysis of
volatility on time series data, b... | 914 | 32,311 |
scikit-bio | skbio/stats/_misc.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 28 | 888 |
scikit-bio | skbio/stats/distance/_utils.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 199 | 5,241 |
scikit-bio | skbio/stats/distance/_permanova.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 603 | 25,330 |
scikit-bio | skbio/stats/distance/_base.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 2,592 | 88,257 |
scikit-bio | skbio/stats/distance/_bioenv.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 236 | 9,374 |
scikit-bio | skbio/stats/distance/_permdisp.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 330 | 13,551 |
scikit-bio | skbio/stats/distance/__init__.py | .py | r"""Distance matrix-based statistics (:mod:`skbio.stats.distance`)
==============================================================
.. currentmodule:: skbio.stats.distance
This module provides functionality for storing, manipulating, and analyzing pairwise
relationships, especially distances, between biological objects... | 214 | 5,319 |
scikit-bio | skbio/stats/distance/_mantel.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 890 | 33,575 |
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