deepC:从兆碱基规模的DNA序列预测Hi-C染色质相互作用的神经网络框架
深层
一个Tensorflow DL框架，用于使用兆碱基规模的DNA序列预测Hi-C染色质相互作用。
描述
该存储库包含核心deepC python代码，R脚本和用于下游分析的功能，以及教程和示例数据的链接。
核心代码在python（v3.5 +）和tensorflow（v1）中实现。 对于下游分析和可视化，我们使用R和自定义函数来处理HiC数据和deepC预测。
要求
python 3.5 +
张量流（tensorflow-gpu）
GPU支持对于预测是更可取的，对于培训来说是必不可少的
其他python模块：
numpy（v1.16.4或以上）
pysam（已通过v0.15.2测试）
pybedtools和已安装的兼容版本的bedtools
R版本3.4.4 +
套餐：
tidyverse（v1.2.1或更高版本）
RColorBrewer（v1.1-2或更高版本）
文件下载
资源详情
[{"title":"（ 54 个子文件 20.73MB ） deepC:从兆碱基规模的DNA序列预测Hi-C染色质相互作用的神经网络框架","children":[{"title":"deepC-master","children":[{"title":"models","children":[{"title":"README.md <span style='color:#111;'> 2.38KB </span>","children":null,"spread":false}],"spread":true},{"title":"formatted_data_links","children":[{"title":"README.md <span style='color:#111;'> 1.13KB </span>","children":null,"spread":false}],"spread":true},{"title":"tensorflow2.1plus_compatibility_version","children":[{"title":"deepCregr.py <span style='color:#111;'> 19.25KB </span>","children":null,"spread":false},{"title":"deepCregr_utility.py <span style='color:#111;'> 19.97KB </span>","children":null,"spread":false},{"title":"run_training_deepCregr.py <span style='color:#111;'> 35.81KB </span>","children":null,"spread":false},{"title":"run_get_saliency.py <span style='color:#111;'> 26.44KB </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 1.68KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_deepCregr.py <span style='color:#111;'> 15.98KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_combination_deepCregr.py <span style='color:#111;'> 13.38KB </span>","children":null,"spread":false}],"spread":true},{"title":"docs","children":[{"title":"logo_1_transparent.png <span style='color:#111;'> 64.75KB </span>","children":null,"spread":false}],"spread":true},{"title":"tensorflow2.0_compatibility_version","children":[{"title":"deepCregr.py <span style='color:#111;'> 18.98KB </span>","children":null,"spread":false},{"title":"deepCregr_utility.py <span style='color:#111;'> 19.70KB </span>","children":null,"spread":false},{"title":"run_training_deepCregr.py <span style='color:#111;'> 35.61KB </span>","children":null,"spread":false},{"title":"run_get_saliency.py <span style='color:#111;'> 26.31KB </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 1.81KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_deepCregr.py <span style='color:#111;'> 15.94KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_combination_deepCregr.py <span style='color:#111;'> 13.37KB </span>","children":null,"spread":false}],"spread":true},{"title":"data_links","children":[{"title":"README.md <span style='color:#111;'> 2.00KB </span>","children":null,"spread":false}],"spread":true},{"title":"LICENSE <span style='color:#111;'> 34.33KB </span>","children":null,"spread":false},{"title":"legacy_version_tf1.8","children":[{"title":"deepCregr.py <span style='color:#111;'> 18.94KB </span>","children":null,"spread":false},{"title":"deepCregr_utility.py <span style='color:#111;'> 19.55KB </span>","children":null,"spread":false},{"title":"run_training_deepCregr.py <span style='color:#111;'> 35.49KB </span>","children":null,"spread":false},{"title":"run_get_saliency.py <span style='color:#111;'> 26.31KB </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 1.70KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_deepCregr.py <span style='color:#111;'> 15.65KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_combination_deepCregr.py <span style='color:#111;'> 13.33KB </span>","children":null,"spread":false}],"spread":true},{"title":"__init__.py <span style='color:#111;'> 109B </span>","children":null,"spread":false},{"title":"tutorials","children":[{"title":"tutorial_predict_and_plot.Rmd <span style='color:#111;'> 23.46KB </span>","children":null,"spread":false},{"title":"tutorial_format_HiC_data_for_deepC.html <span style='color:#111;'> 1.19MB </span>","children":null,"spread":false},{"title":"tutorial_format_HiC_data_for_deepC.Rmd <span style='color:#111;'> 7.77KB </span>","children":null,"spread":false},{"title":"example_variant.bed <span style='color:#111;'> 26B </span>","children":null,"spread":false},{"title":"test_variant_out","children":[{"title":"class_predictions_predict_variant_provided_1_chr17_71706322_71706671.txt <span style='color:#111;'> 279.40KB </span>","children":null,"spread":false}],"spread":false},{"title":"tutorial_predict_and_plot.html <span style='color:#111;'> 26.09MB </span>","children":null,"spread":false},{"title":"hg19_chrom_sizes.txt <span style='color:#111;'> 1.92KB </span>","children":null,"spread":false},{"title":"tutorial_train_a_model.md <span style='color:#111;'> 5.35KB </span>","children":null,"spread":false},{"title":"example_region_short.bed <span style='color:#111;'> 34B </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 1.18KB </span>","children":null,"spread":false},{"title":"test_predict_out","children":[{"title":"class_predictions_predict_provided_1_chr17_71000000_71999999.txt <span style='color:#111;'> 552.98KB </span>","children":null,"spread":false}],"spread":false}],"spread":false},{"title":"tensorflow1_version","children":[{"title":"deepCregr.py <span style='color:#111;'> 19.21KB </span>","children":null,"spread":false},{"title":"deepCregr_utility.py <span style='color:#111;'> 19.93KB </span>","children":null,"spread":false},{"title":"run_training_deepCregr.py <span style='color:#111;'> 35.77KB </span>","children":null,"spread":false},{"title":"run_get_saliency.py <span style='color:#111;'> 26.41KB </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 1.55KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_deepCregr.py <span style='color:#111;'> 15.94KB </span>","children":null,"spread":false},{"title":"run_deploy_shape_combination_deepCregr.py <span style='color:#111;'> 13.35KB </span>","children":null,"spread":false}],"spread":true},{"title":".gitignore <span style='color:#111;'> 1.17KB </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 3.77KB </span>","children":null,"spread":false},{"title":"helper_for_preprocessing_and_analysis","children":[{"title":"functions_for_HiC.R <span style='color:#111;'> 30.12KB </span>","children":null,"spread":false},{"title":"reference_manual_deepC_R_utility.pdf <span style='color:#111;'> 136.25KB </span>","children":null,"spread":false},{"title":"example_head_10lines_data_K562_5kb_regression.txt <span style='color:#111;'> 4.27KB </span>","children":null,"spread":false},{"title":"prepare_query_table.pl <span style='color:#111;'> 1.34KB </span>","children":null,"spread":false},{"title":"functions_for_deepC.R <span style='color:#111;'> 49.55KB </span>","children":null,"spread":false},{"title":"match_query_table.pl <span style='color:#111;'> 1.46KB </span>","children":null,"spread":false},{"title":"README.md <span style='color:#111;'> 1.64KB </span>","children":null,"spread":false}],"spread":true}],"spread":false}],"spread":true}]
评论信息
其他资源
- 新闻发布系统需求文档，详细的介绍，有e-r图
- 麦克风阵列仿真的源代码
- 30个经典的C++实例
- mysql+javaweb网上书店系统
- High Performance MySQL_3rd_edition
- stm32F4固件库2.11.0版本;STM32F4xx_DFP.2.11.0.pack
- 13.56MHZ 射频 非接触 NFC RC522 500开发设计资料（ISO14443）.zip
- C语言编程实验sy1-3.c
- antd-ui-components-源码
- jdk-8u77-windows-i586.exe
- 备忘录：React浏览器记忆游戏-源码
- Manual.pdf
- default.conf
- swagger-word文档生成程序.rar
- 操作系统进程调度C++代码实现
- 湖南科技大学 选课助手
- LL1文法消除左递归编译原理mfc实现（完整版)
- VC++多人聊天室
- 索尼刷机基带
- Computer Graphics for Java Programmers 2nd
- video demystified(5th)中文版--视频技术手册：1~6章
- zip文件压缩解压库文件（整理过的）
- pyexcel技术文档
- C++实现找出两个字符串中最大的公共子串
免责申明
【只为小站】的资源来自网友分享，仅供学习研究，请务必在下载后24小时内给予删除，不得用于其他任何用途，否则后果自负。基于互联网的特殊性，【只为小站】 无法对用户传输的作品、信息、内容的权属或合法性、合规性、真实性、科学性、完整权、有效性等进行实质审查；无论 【只为小站】 经营者是否已进行审查，用户均应自行承担因其传输的作品、信息、内容而可能或已经产生的侵权或权属纠纷等法律责任。
本站所有资源不代表本站的观点或立场，基于网友分享，根据中国法律《信息网络传播权保护条例》第二十二条之规定，若资源存在侵权或相关问题请联系本站客服人员，zhiweidada#qq.com，请把#换成@，本站将给予最大的支持与配合，做到及时反馈和处理。关于更多版权及免责申明参见 版权及免责申明
本站所有资源不代表本站的观点或立场，基于网友分享，根据中国法律《信息网络传播权保护条例》第二十二条之规定，若资源存在侵权或相关问题请联系本站客服人员，zhiweidada#qq.com，请把#换成@，本站将给予最大的支持与配合，做到及时反馈和处理。关于更多版权及免责申明参见 版权及免责申明