Resources¶

Brief Description¶

Click on the “Resources” link in the main menu to view training data statistics, quality control information, and model evaluation results. In addition, we provide links to download the reference genomes, the trained models and files for training models.

Please note: We are still analyzing the ATAC-seq data we generated from multiple tissues of grass species. We have provided lists of OCRs obtained from these ATAC-seq data so that researchers can use it to reproduce the results of PlantDeepSEA. However, please do not use these lists for genome-scale analyses, until the publication of our article on data analysis (by May 2022 at the latest). Or contact us for permission. Users who download data from this site are considered to have accepted this statement.

Reference Genome Information (Download from Google Drive)¶

variety	Species	Version	Reference link
Arabidopsis	Arabidopsis thaliana	TAIR10.1	Download link
Rice	Oryza sativa	MSU v7.0	Download link
Rice	Oryza sativa	MH63 RS2	Download link
Rice	Oryza sativa	ZS97 RS2	Download link
Brachypodium	Brachypodium distachyon	Bd21-3 v1.1	Download link
Foxtail millet	Setaria italica	v2.0	Download link
Sorghum	Sorghum bicolor	v3.1.1	Download link
Mazie	Zea mays	AGPv4	Download link

Reference Genome Information (Download from Baidu Cloud Disk Drive)¶

variety	Species	Version	Reference link
Arabidopsis	Arabidopsis thaliana	TAIR10.1	链接：https://pan.baidu.com/s/1TvqpN94yE6gq7VHVRNt6kA?pwd=iv43 提取码：iv43
Rice	Oryza sativa	MSU v7.0	链接: https://pan.baidu.com/s/1SYpyzJLd6X_3sTVoTbyxbw 提取码: tdgi
Rice	Oryza sativa	MH63 RS2	链接：https://pan.baidu.com/s/1uXqWbSdipnNHfckH6xOZoA?pwd=7fed 提取码：7fed
Rice	Oryza sativa	ZS97 RS2	链接：https://pan.baidu.com/s/1Xm8GoRQ2wCt1aSjU7DEqUQ?pwd=bhtw 提取码：bhtw
Brachypodium	Brachypodium distachyon	Bd21-3 v1.1	链接: https://pan.baidu.com/s/1hiUYOE9g3KwtDucUkRkPTw 提取码: r4ka
Foxtail millet	Setaria italica	v2.0	链接：https://pan.baidu.com/s/1qjwnowHMEf_psOLpTgEo0g?pwd=4m10 提取码：4m10
Sorghum	Sorghum bicolor	v3.1.1	链接：https://pan.baidu.com/s/1AqbUPws9AyTtjnBv3vUMmQ?pwd=3j0q 提取码：3j0q
Mazie	Zea mays	AGPv4	链接：https://pan.baidu.com/s/1Ppexb6mzC_FtfvIzfYb4vw?pwd=1xf8 提取码：1xf8

Trained model¶

variety	Reference link
Arabidopsis	Download link
Zhenshan 97	Download link
Minghui 63	Download link
Brachypodium	Download link
Foxtail millet	Download link
Sorghum	Download link
Mazie	Download link

Training data¶

variety	Reference link
Arabidopsis	Download link
Zhenshan 97	Download link
Minghui 63	Download link
Brachypodium	Download link
Foxtail millet	Download link
Sorghum	Download link
Mazie	Download link

Training config files¶

variety	Reference link
Arabidopsis	Download link
Zhenshan 97	Download link
Minghui 63	Download link
Brachypodium	Download link
Foxtail millet	Download link
Sorghum	Download link
Mazie	Download link

Model structure¶

model name	Reference link
DeeperDeepSEA	Download link

This model structure is Selene’s DeeperDeepSEA structure .

A guide to applying the model locally¶

You can click here to see how the models are trained and how to apply the trained models provided in PlantDeepSEA locally.