معرفی شرکت ها

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome

ویژگی	مقدار
سیستم عامل	-
نام فایل	ConsTADs-1.0.0
نام	ConsTADs
نسخه کتابخانه	1.0.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	-
ایمیل نویسنده	Dachang Dang <dangdachang@163.com>
آدرس صفحه اصلی	-
آدرس اینترنتی	https://pypi.org/project/ConsTADs/
مجوز	MIT License Copyright (c) [year] [fullname] Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 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.

# ConsTADs Topologically associating domains (TADs) have emerged as basic structural and functional units of genome organization, and have been determined by many computational methods from Hi-C contact maps. However, the TADs obtained by different methods vary greatly, which makes the accurate determination of TADs a challenging issue and hinders subsequent biological analyses about their organization and functions. This project is about comparing different TAD-calling methods, building the TAD separation landscape and finding the consensus TADs from results of multiple methods. ## Overview This computational framework consists of three main steps, including: 1. Running different TAD-calling methods on the same Hi-C contact map; 2. Collecting the TAD boundaries identified by each method and performing boundary voting; 3. Refining the boundary score profile based on the contrast P-values of chromatin interactions using three operations, Add, Filter and Combine, to construct the TAD separation landscape. <img src="./TAD%20separation%20landscape%20application.png" width="65%" height="65%" /> The TAD separation landscape can be used in scenarios such as: 1. Comparing domain boundaries across multiple cell types for discovering conserved and divergent topological structures; 2. Deciphering three types of boundary regions with diverse biological features; 3. Identify Consensus Topological Associating Domains (ConsTADs). <img src="./TAD%20separation%20landscape%20construction.png" width="65%" height="65%"/> ## Getting start ### Installation It's recommended to create a conda environment: ```shell conda create -n ConsTADs python=3.7 conda activate ConsTADs ``` Install required packages: ```shell pip install -r requirements.txt ``` Install ConsTADs by PyPI: ```shell pip install ConsTADs ``` Install from source code: ```shell git clone https://github.com/zhanglabtools/ConsTADs.git cd ConsTADs python setup.py build python setup.py install ``` ### Example usage See [ConsTADs usage.ipynb](./ConsTADs%20usage.ipynb). ### Support If you are having issues, please let us know. We have a mailing list located at: * dangdachang@163.com ### Citation If ConsTADs is useful for your research, consider citing our preprint: > Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome. > Dachang Dang, Shao-Wu Zhang, Ran Duan, Shihua Zhang. > bioRxiv 2022.08.08.503155; **doi:** https://doi.org/10.1101/2022.08.08.503155

نیازمندی

مقدار	نام
-	matplotlib>=3.5.0
-	numpy>=1.20.3
-	pandas>=1.3.5
-	scikit-learn>=1.0
-	scipy>=1.7.3
-	tqdm>=4.64.1

زبان مورد نیاز

مقدار	نام
>=3.7	Python

نحوه نصب

نصب پکیج whl ConsTADs-1.0.0:

pip install ConsTADs-1.0.0.whl

نصب پکیج tar.gz ConsTADs-1.0.0:

pip install ConsTADs-1.0.0.tar.gz