crested

View on PyPIReverse Dependencies (0)

1.3.0 crested-1.3.0-py3-none-any.whl

Wheel Details

Project: crested
Version: 1.3.0
Filename: crested-1.3.0-py3-none-any.whl
Download: [link]
Size: 160572
MD5: e67a5b2fe313c0394bb08723c4332a90
SHA256: 99812de07720e999873a9866767c214855edcc60fe0ed65b333e5faa43368d44
Uploaded: 2025-02-13 16:02:11 +0000

dist-info

METADATA

Metadata-Version: 2.4
Name: crested
Version: 1.3.0
Summary: CREsted: Cis-Regulatory Element Sequence Training, Explanation, and Design
Author: Stein Aerts Lab
Maintainer-Email: Lukas Mahieu <lukas.mahieu[at]kuleuven.be>
Project-Url: Documentation, https://crested.readthedocs.io/
Project-Url: Source, https://github.com/aertslab/crested/
Project-Url: Home-page, https://github.com/aertslab/crested/
License: Academic Non-commercial Software License Agreement The Licensed Software is developed by and on behalf of the Laboratory of Computational Biology of VIB-KU Leuven and is owned by VIB vzw, located at Rijvisschestraat 120, B-9052 Zwijnaarde, Belgium (hereinafter referred to as "VIB"). By downloading or installing the Licensed Software, the user agrees with the terms and conditions below. Definitions “Licensed Software” shall mean CREsted as available on GitHub. "Effective Date" shall mean the date on which you download or install CREsted (as available on GitHub) on your system and which provide you access to the CREsted tool. “Commercial Purposes” shall include (1) the use of Licensed Software to provide a service, information or data that is directly or indirectly conveyed to any third party against compensation, (2) any type of transfer of the Licensed Software for compensation, and (3) any other use of Licensed Software that supports commercial entities. License 1. Licensed Software is the work of the Aerts lab. The copyright in Licensed Software is owned by VIB. 2. Subject to the terms and conditions of this Agreement, VIB hereby grants and the user accepts a non-exclusive, non-transferable license to use the Licensed Software for strictly internal academic research use only, on your own behalf or on behalf of your institution, and not for Commercial Purposes. 3. The user confirms to be an academic user. For academic users, there is no license fee. 4. The user shall acknowledge VIB as the provider of Licensed Software and shall include the following reference “Kempynck et al., CREsted: Cis Regulatory Element Sequence Training, Explanation, and Design. Zenodo (2024) 10.5281/zenodo.13320756: 2024-08” in any manuscript describing data obtained using Licensed Software. 5. This license does not entitle the user to receive from VIB hard-copy documentation, technical support, telephone assistance, or enhancements or updates to the Licensed Software, and nothing contained herein shall be interpreted as to require VIB, its faculty, employees or students to provide maintenance, installation services, debugging, consultation or end-user support of any kind. 6. The title and copyright to Licensed Software and any associated programs and documentation shall remain with VIB. The user agrees to preserve the same. 7. The user agrees not to make any copies of Licensed Software except for use in the user’s laboratory, without VIB’s prior written consent. The user agrees to place the appropriate copyright notice on any such copies. 8. The user shall not distribute Licensed Software to other laboratories within user’s institution. The user shall not transfer Licensed Software to another location or person outside of user’s institution without VIB’s prior and written permission. 9. The user shall not market or otherwise benefit commercially from any product utilizing any portion of Licensed Software, nor any derivative works of Licensed Software, without first entering into a separate commercial license with VIB. 10. Except as otherwise expressly permitted in this Agreement, the user must not (i) modify or create any derivative works of the Licensed Software or documentation, including customization, translation or localization; (ii) decompile, disassemble, reverse engineer, or otherwise attempt to derive the source code for the Licensed Software; (iii) remove or alter any trademark, logo, copyright or other proprietary notices, legends, symbols or labels in the Licensed Software. 11. The user acknowledges that the Licensed Software is proprietary to VIB. The software code shall be treated as trade secrets and confidential information of VIB, and the user agrees to use all reasonable efforts to hold the same in confidence. The user’s obligation for confidentiality shall not extend to any information which (i) is or becomes generally available to the public, (ii) is already known to or subsequently disclosed by third parties to the user and at its free disposal, or (iii) is independently developed by the user or its affiliates without the use of the confidential information disclosed by VIB, or (iv) is required by law or legal process to be disclosed. 12. The user acknowledges that Licensed Software is a research tool and provided free of charge, it is only provided “as is”. VIB makes no representations or warranties of any type whatsoever, express or implied, regarding the Licensed Software. VIB expressly disclaims all representations and warranties regarding the Licensed Software, including but not limited to any representations or warranties of merchantability or fitness for any particular application or that the use of the Licensed Software will not infringe any patents, copyrights or trademarks or other rights of third parties, or any warranty that the rights and licenses granted hereunder comprise all the rights and licenses necessary or desirable to use the Licensed Software for internal non-commercial research purposes as permitted by this Agreement. The entire risk as to the quality and performance of the Licensed Software is borne by the user. 13. VIB shall not be responsible for losses of any kind resulting from the use of Licensed Software, and can in no way provide compensation for any losses sustained, including but not limited to, any obligation, liability, right, claim or remedy for tort, or for any actual or alleged infringement of patents, copyrights, trade secrets, or similar rights of third parties, nor any business expense, machine downtime or damages caused by any deficiency, defect or error in Licensed Software or mal-function thereof, nor any incidental or consequential damages, however caused. 14. The user will indemnify, defend and hold harmless VIB, its directors, officers, employees and agents from and against all liability, losses, damages and expenses (including attorney’s fees and costs) arising out of any claims, demands, actions or other proceedings made or instituted by any third party against any of them and arising out of or relating to any breach of this Agreement by the user, or any use of the Licensed Software by the user, except insofar as such claims or liability result from VIB’s gross negligence or willful misconduct. 15. This Agreement and the license rights granted herein shall become effective as of the date the user downloaded the Licensed Software and shall continue in full force until the user deletes the Licensed Software and any and all related files from the user’s computing system, unless terminated in accordance with this Section. Upon one party's breach of any agreement, covenant, or representation made in this Agreement, the agreement will automatically end thirty (30) days after such breach. Either party shall have the right, at any time, to terminate this Agreement without cause by written notice to the other party specifying the date of termination. Upon termination, the user shall destroy all full and partial copies of the Licensed Software. The user shall forward written notice to VIB that all programs containing Licensed Software have been deleted from all computer libraries and storage or memory devices and are no longer stored therein. 16. This Agreement shall be construed in accordance with the laws of Belgium. The courts of Belgium shall have exclusive jurisdiction. 17. The parties agree that this Agreement is the complete and exclusive agreement among the parties and supersedes all proposals and prior agreements whether written or oral, and all other communications among the parties relating to the subject matter of this Agreement. This Agreement cannot be modified except in writing and signed by both parties. Failure by either party at any time to enforce any of the provisions of this Agreement shall not constitute a waiver by such party of such provision nor in any way affect the validity of this Agreement. 18. The invalidity of singular provisions does not affect the validity of the entire understanding. The parties are obligated, however, to replace the invalid provisions by a regulation, which comes closest to the economic intent of the invalid provision. The same shall apply mutatis mutandis in case of a gap. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Requires-Python: >=3.9
Requires-Dist: anndata
Requires-Dist: biothings-client (<0.4.0)
Requires-Dist: keras (>=3.4.0)
Requires-Dist: logomaker
Requires-Dist: loguru
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pooch
Requires-Dist: pybigtools (>=0.2.0)
Requires-Dist: pysam
Requires-Dist: scanpy
Requires-Dist: scikit-learn
Requires-Dist: seaborn
Requires-Dist: tqdm
Requires-Dist: wandb (>=0.12.10)
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: pydocstyle; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: twine (>=4.0.2); extra == "dev"
Requires-Dist: docutils (!=0.18.*,!=0.19.*,>=0.8); extra == "doc"
Requires-Dist: ipykernel; extra == "doc"
Requires-Dist: ipython; extra == "doc"
Requires-Dist: modisco-lite; extra == "doc"
Requires-Dist: myst-nb; extra == "doc"
Requires-Dist: pandas; extra == "doc"
Requires-Dist: ruff; extra == "doc"
Requires-Dist: sphinx-autodoc-typehints; extra == "doc"
Requires-Dist: sphinx-book-theme (>=1.0.0); extra == "doc"
Requires-Dist: sphinx-copybutton; extra == "doc"
Requires-Dist: sphinx (>=4); extra == "doc"
Requires-Dist: sphinxcontrib-bibtex (>=1.0.0); extra == "doc"
Requires-Dist: sphinxext-opengraph; extra == "doc"
Requires-Dist: tensorflow; extra == "doc"
Requires-Dist: anndata; extra == "test"
Requires-Dist: coverage; extra == "test"
Requires-Dist: genomepy; extra == "test"
Requires-Dist: pytest; extra == "test"
Provides-Extra: dev
Provides-Extra: doc
Provides-Extra: test
Description-Content-Type: text/markdown
License-File: LICENSE
[Description omitted; length: 4853 characters]

WHEEL

Wheel-Version: 1.0
Generator: hatchling 1.27.0
Root-Is-Purelib: true
Tag: py3-none-any

RECORD

Path Digest Size
crested/__init__.py sha256=iwwiRo0-LejlAZQ7ZeVLzcZQh16g9Pt-fw5iwsJiY_0 1064
crested/_conf.py sha256=OW85OQ81NyVFYLztZV79HEh-b_NRG6ZcPlQw3zT04Q4 99
crested/_datasets.py sha256=AEDhEVmFBtTpHHZG6xeao1JpMKD6HxIurRS89s7_blA 13691
crested/_genome.py sha256=Vro1byAC7etyF4oD6g1hBjdFnVmWJCrBUfXGxg_4n3U 8157
crested/_io.py sha256=fasKxhPoRRaEJeHLaWjzzj_-2ZI2g9XcE_I3shzvuGA 23167
crested/pl/__init__.py sha256=USE2FoDJpcx_PgSbE-EhQr8fm9zRggKHpIC5q2g2G4Q 120
crested/pl/_utils.py sha256=Mum8mTpaa0MHalTyK4VgXuHdiki8rJS9dcq6M3dHqoI 2906
crested/pl/bar/__init__.py sha256=ku6FKkS4QFHsUYT7plDhjcCU3epmu124k98rlbrWbPE 152
crested/pl/bar/_normalization_weights.py sha256=0gXqQQwNQ1A2wSlrQ-9b-Rukfy5zNw2LG_kVkM58I0U 1707
crested/pl/bar/_region.py sha256=HksIgeZgR_SGx3vwZuVVblFyOUdwPPhIIh5Dh6uTonY 7397
crested/pl/heatmap/__init__.py sha256=pQv_HTEnTrJ6C9T5_nZw9HPt7JEPhtNlWPwM0NZK6f8 112
crested/pl/heatmap/_correlations.py sha256=YN5wI36ptFVWiCzTnDpEYt4PIi1irQ3IJDBOKm8JHVA 6268
crested/pl/hist/__init__.py sha256=HrpS_-sPJCY07ijsA_Ii_l6wdApZDQzzcsO702-Rif0 117
crested/pl/hist/_distribution.py sha256=yqYUppkc3IuZ3-ZnI8jSGVptMmXTZGQ1OlHemIHb_q4 3762
crested/pl/hist/_locus_scoring.py sha256=PrciZV0ArAH-HvfngxzuSx8_ynqWb0hzb9ZtCOoQhYY 4266
crested/pl/patterns/__init__.py sha256=V0wK_JJceA_VCV0De4qkOWad1ZXB2hpH6tnRXXBhz6M 2103
crested/pl/patterns/_contribution_scores.py sha256=L6ZGWhtY4zb8qFaf94jfBs6Ng7HEnKzzx10Bmv8jUTU 7181
crested/pl/patterns/_enhancer_design.py sha256=Kw0zsh5BtVvD5hVmDApHF3EG2w7IQTQCoEP04HSHj9k 16587
crested/pl/patterns/_modisco_results.py sha256=cJrLwTNBNnIX5vq9WL52MbZQT0znsnZ-wxjfrfXs1yk 31071
crested/pl/patterns/_utils.py sha256=Aj0w2JADn3f3qSWdDtGzgNuEuOGzGHDV-3NBKxXrfwM 5383
crested/pl/scatter/__init__.py sha256=RtDscjF3ESIR02eFxe6p5x5lOfo_41mO2XsWJV0sQpk 79
crested/pl/scatter/_class_density.py sha256=jo61ujwbxPxrmxlT_Ap2vu84yBxaabVFdTpnXx_GDzo 6023
crested/pp/__init__.py sha256=ArXq6AmqsTdMa6ilG098-KZ81rfnli_r4Z7WP0jWuGU 268
crested/pp/_filter.py sha256=Fsai300YXiE_QZ2AFCjYsGjxsEJbXcqcgPuUW_a0BYQ 5937
crested/pp/_normalization.py sha256=N7F2Sg2GBGxwzhkj0-CbDNSyp3xvKzrE1a5RPYpOfzc 3702
crested/pp/_regions.py sha256=6v0L_to8SeLEB9iiK9Tg5txQs7FXTJ_DlS5spChfxqQ 3398
crested/pp/_split.py sha256=LbT1o5aa9PMe0MFetY8UWq3ElEt3rHEFW6F23zn9xaA 9903
crested/pp/_utils.py sha256=K9Q55X3wm1cF_s0ubv_uRYVyqGzY5W14v8tsrTZY9yo 2719
crested/tl/__init__.py sha256=H8nv_JTBU7c0cJa28SDv_zpfeHvmDUp0CuL6Ej1azug 1296
crested/tl/_configs.py sha256=KNEXD6reAwu9RJGMab_32cB9-lRVJJaOlM0Fzi6RLwo 6103
crested/tl/_crested.py sha256=f1usQvR7OJUTJSy7QrLEP42XtSobFYRCjVfRSrb06m4 82757
crested/tl/_explainer_tf.py sha256=kuLFCQOey-mvdmKUZRj8rrkRJvpHV6CUenBZ55Ua2c4 7928
crested/tl/_explainer_torch.py sha256=2FggJBE8g4EpIgLF7tqUbWYrO0kfZx8ERUd-lMvwrMU 8007
crested/tl/_tools.py sha256=mMrIJgJ4kJwOy8hFf_jarnP3--tJHkL1geH6AElvlG4 35603
crested/tl/_utils.py sha256=1xgTKUyXynXDuIMfcYwgBX6egUm4NpUqkQcrCVnSWLA 2285
crested/tl/data/__init__.py sha256=sjRMauKkPZymYO98socTEKnmdaXBvdoazfyGN3F5sdo 164
crested/tl/data/_anndatamodule.py sha256=7_19cu8aoqbDJyHpJ5X-nfqG9hKyN5gnmrIwHMsoOM4 8116
crested/tl/data/_dataloader.py sha256=IZS0r3PVk6K3_VhLbWpo_jpenh6Iagex-Bc06KP9gDA 3531
crested/tl/data/_dataset.py sha256=fEGY1OLJo799W8qscyYAA8DSh4QRTwmIqZTvHiJ5DNE 16058
crested/tl/losses/__init__.py sha256=ab3repbDhNnxJIF8N5tRp6OUZbbuJRreQ83DeSrYMbs 209
crested/tl/losses/_cosinemse.py sha256=ATfk0eQpyPbGs7s43UJA2d1UPWq8_1ywMC1VBPqz0So 2935
crested/tl/losses/_cosinemse_log.py sha256=KY7f3JkvrAj_wLifjocygrwYV4sfyEjtzYWXGCdST4w 3315
crested/tl/losses/_poisson.py sha256=CbACr1neQ8XxtpvECtG_ssHcZf2mO309JKE70jRzDHM 2150
crested/tl/losses/_poissonmultinomial.py sha256=Mes1jJM2dm2e_U09LDHtD2OtEmXmjpaDtWWEIiCaBJ4 3206
crested/tl/metrics/__init__.py sha256=TEOr8DcKJzek2T-pqwI8OAgcW2sU3-8syXX9SToxOu4 296
crested/tl/metrics/_concordancecorr.py sha256=qhQhfz9Y2WZYDNkH3RPxH81ozeN5XH-RM5hbn5UF5Ec 2675
crested/tl/metrics/_pearsoncorr.py sha256=DjCmv3kLMRAgv8pzlxQVoIS64gURtAi7NHQEqTG-Ivk 2438
crested/tl/metrics/_pearsoncorrlog.py sha256=akSrL4jYGc-3XDfbe5HRPSfo8YS49AKwZZFzo_-cl3Q 2721
crested/tl/metrics/_spearmancorr.py sha256=JOG8cjC9lws7QxQCdcmZcuQZfgYKB7Ngtv8JEr-A9Ig 3465
crested/tl/metrics/_zeropenalty.py sha256=MJ6eBNylGC6dYllfQ1VaeoR-bHhhFjdI3nSdKIw1Oqw 1951
crested/tl/modisco/__init__.py sha256=IWgZf602PrGSyK1ozD2FFTRyGQ6ratIibclB0Hp5MZ0 482
crested/tl/modisco/_modisco_utils.py sha256=42b1h7NFBvJUkA2sZO-chXDbIvfIt4es7ZVjhDgS6uw 15097
crested/tl/modisco/_tfmodisco.py sha256=ieW5E4HFB8JYUwId075P3K_20fGjEhpSfBIIkATuuZM 48529
crested/tl/zoo/__init__.py sha256=v6DH5WCwb72rxiDdjQEJ8FrrMNIM_8woA5oZZhuUxoI 351
crested/tl/zoo/_basenji.py sha256=53P60fiFeXwEvkp4Au6Wq6ADlBdVSQvGA_4gdOcqC8A 2836
crested/tl/zoo/_borzoi.py sha256=dmzxCtpMQPSA3JOfEdzj2JlpUdDpIJlpX_oovd-yoKU 10157
crested/tl/zoo/_chrombpnet.py sha256=ihqkwMrteuJtcuYUhElQKsVTMNRwY4OaZ4O4JryuOhg 4667
crested/tl/zoo/_chrombpnet_decoupled.py sha256=7ahK1JS89yJCOlbPASFOwI87nXrWkVQfhkB46okuPJg 5112
crested/tl/zoo/_deeptopic_cnn.py sha256=_kKh7VT66KI0VakyEC-gpYfqnktxnY1sBEAtekGQHho 3858
crested/tl/zoo/_deeptopic_lstm.py sha256=Nlg1Z1QoJJBLXlokD9FldSupXEcr3V462mZBZVM4IWM 3602
crested/tl/zoo/_enformer.py sha256=nAQgO9t1MHYmONVQb_0eaqjmEyBI3dcLmBANtv6KoW0 8731
crested/tl/zoo/_simple_convnet.py sha256=Vq01S7UcmV6CCfHuHHMu-yZ2OjGMttUKHvGvdvN2_oM 3798
crested/tl/zoo/utils/__init__.py sha256=L9QKRnKHmxKNs8OJKJg1Z1Ir1NNeaKa79-cNvcMQqys 116
crested/tl/zoo/utils/_attention.py sha256=gN0kyc_EB7zFQsx6FwQaKx63EwLAyHzw7mSTtxay31E 22601
crested/tl/zoo/utils/_layers.py sha256=qdMJqqw4Fp3qY2UjL9tq7-TjXBu7zlTNL5XhJUGhhZo 20279
crested/utils/__init__.py sha256=EW_IiCLDSSixCHlYqVnd24r5n-LLzVqPr6VSmS6QyyE 436
crested/utils/_logging.py sha256=078_DZKvyvDu5TfOffE6WRBijyUWSjDHKEvJ3sUc6g0 1214
crested/utils/_model_utils.py sha256=bNOLTGkrxKG5awMQouCrR-Xi6LSmYrYDiPnZiXTuOZ8 1142
crested/utils/_seq_utils.py sha256=_u35ABV-4uOr0RDUkYQ3tFyx90VSBFQkww6zX7TTz5E 7166
crested/utils/_utils.py sha256=rpugCIxcz5Wx4u3xEIhi17p_N-IXhKKoc1-jxH5bVWM 14458
crested-1.3.0.dist-info/METADATA sha256=LbQ42ZwitOVm4dgmaZiGff5zoKdf0kkcZDSqL6EecUA 15976
crested-1.3.0.dist-info/WHEEL sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ 87
crested-1.3.0.dist-info/licenses/LICENSE sha256=3ygvJOgiGCTGsPjoWUh7XoznuPEZmiF2WSCT6RyIJMQ 8748
crested-1.3.0.dist-info/RECORD