[{"_1":2,"_152":-5,"_153":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_131":132},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":-5,"_85":86,"_124":-5,"_125":11,"_126":17,"_127":11,"_128":-5,"_129":130},"canonicalUrl","https://hub.docker.com/r/lsbnb/seashell/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","lsbnb","reponame","seashell","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":70,"_75":11,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2021-06-27T05:39:55.987617Z","description","","is_private","last_updated","2022-01-12T09:42:47.180971Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",1063,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# Seashell v1.0.2\nThis is the first version of the R/Shiny-based **Seashell** web application. \nThis image is provided by Institute of Information Science, Academia Sinica, TAIWAN.\n### Contact information:\n##### Chung-Yen Lin (cylin@iis.sinica.edu.tw); LAB website: http://eln.iis.sinica.edu.tw\n### Team members:\n##### Bo-Yi Yu (boy65061120@iis.sinica.edu.tw )\n##### Chih-Wei Huang (tima@iis.sinica.edu.tw)\n##### Chia-Hsien Chuang (t050508@gmail.com)\n------\n\n# System Structure\n![enter image description here](https://eln.iis.sinica.edu.tw/lims/files/all/seashell/function_seashell.png)\n### \n![enter image description here](https://eln.iis.sinica.edu.tw/lims/files/all/seashell/seashell_docker_ps.png)\n\n# Usage\n## 1. Set up docker environment\n\n### 1-1. Create required folders for input and output files\n```\n### Linux or macOS system (Type below scripts)\n mkdir -m 777 ./my_dir ./my_dir/ref ./my_dir/ref/cellranger_ref ./my_dir/ref/zumi_ref ./my_dir/input ./my_dir/output ./my_dir/exps ./my_dir/meta\n### Windows system (Open PowerShell and type below scripts)\n 'input','output','meta','exps' | % {New-Item -Name \".\\my_dir\\$_\" -ItemType 'Directory'}\n 'cellranger_ref','zumi_ref' | % {New-Item -Name \".\\my_dir\\ref\\$_\" -ItemType 'Directory'}\n```\n\n### 1-2. Data hierarchy\n

\nmy_dir/  \n|----- input/  \n|      |----- folder1/  \n|      |              |----- R1.fastq  \n|      |              |----- R2.fastq \n|      |----- folder2/  \n|      |              |----- R3.fastq  \n|      |              |----- R4.fastq \n|  \n|----- ref/\n|      |----- cellranger_ref/\n|      |\t\t|-----hg38/\n|      |\t\t|-----mm10/\n|      |\t\t\n|      |----- zumis_ref/\n|      \t\t|-----hg38/\n|      \t\t|-----mm10/ \t\t\n| \n|----- output/\n| \n|----- meta/\n|----- exps/\n

\n\n### 1-3. Download reference files from docker image (There are four reference folders. You can just download which you need.) \n```\n### Reference for run CellRanger hg38\ndocker pull lsbnb/seashell_ref_cellranger_hg38\ndocker run --name=seashell_ref_cellranger_hg38 -dti lsbnb/seashell_ref_cellranger_hg38 /bin/bash\n#### Linux or macOS system \n docker cp seashell_ref_cellranger_hg38:/home/cellranger_ref/hg38 $(pwd)/my_dir/ref/cellranger_ref\n#### Windows system \n $curPath = (Get-Location).path + '\\my_dir\\ref\\cellranger_ref'\n docker cp seashell_ref_cellranger_hg38:/home/cellranger_ref/hg38 $curPath\ndocker rm -f seashell_ref_cellranger_hg38\n\n### Reference for run CellRanger mm10\ndocker pull lsbnb/seashell_ref_cellranger_mm10 \ndocker run --name=seashell_ref_cellranger_mm10 -dti lsbnb/seashell_ref_cellranger_mm10 /bin/bash\n#### Linux or macOS system \n docker cp seashell_ref_cellranger_mm10:/home/cellranger_ref/mm10 $(pwd)/my_dir/ref/cellranger_ref\n#### Windows system \n $curPath = (Get-Location).path + '\\my_dir\\ref\\cellranger_ref'\n docker cp seashell_ref_cellranger_mm10:/home/cellranger_ref/mm10 $curPath\ndocker rm -f seashell_ref_cellranger_mm10\n\n### Reference for run zUMIs hg38\ndocker pull lsbnb/seashell_ref_zumi_hg38 \ndocker run --name=seashell_ref_zumi_hg38 -dti lsbnb/seashell_ref_zumi_hg38 /bin/bash\n#### Linux or macOS system \n docker cp seashell_ref_zumi_hg38:/home/zumi_ref/hg38 $(pwd)/my_dir/ref/zumi_ref\n#### Windows system \n $curPath = (Get-Location).path + '\\my_dir\\ref\\zumi_ref'\n docker cp seashell_ref_zumi_hg38:/home/zumi_ref/hg38 $curPath\ndocker rm -f seashell_ref_zumi_hg38\n\n### Reference for run zUMIs mm10\ndocker pull lsbnb/seashell_ref_zumi_mm10 \ndocker run --name=seashell_ref_zumi_mm10 -dti lsbnb/seashell_ref_zumi_mm10 /bin/bash\n#### Linux or macOS system \n docker cp seashell_ref_zumi_mm10:/home/zumi_ref/mm10 $(pwd)/my_dir/ref/zumi_ref\n#### Windows system \n $curPath = (Get-Location).path + '\\my_dir\\ref\\zumi_ref'\n docker cp seashell_ref_zumi_mm10:/home/zumi_ref/mm10 $curPath\ndocker rm -f seashell_ref_zumi_mm10\n```\n\n### 1-4. Run the docker\n```\ndocker pull lsbnb/seashell:latest\n### Linux or macOS system \n docker run --name=seashell -dti -p 8080:8080 -p 8081:80 -v $(pwd)/my_dir:/home/my_dir lsbnb/seashell /bin/bash\n### Windows system \n $curPath = (Get-Location).path + '\\my_dir:/home/my_dir'\n docker run --name=seashell -dti -p 8080:8080 -p 8081:80 -v $curPath lsbnb/seashell /bin/bash\n```\n\n## 2. Run SeaShell_Data by command mode\n### 2-1. CellRanger 3.0.2 -> output = 'matrix.mtx.gz', 'features.tsv.gz', 'barcodes.tsv.gz', and 'web_summary.html'\n```\n### Create one folder and put your input files into ./my_dir/input/ \ndocker exec seashell /home/apps/cellranger-3.0.2/cellranger count --id=output_folder1 \\\n--transcriptome=/home/my_dir/ref/cellranger_ref/hg38 \\\n--fastqs=/home/my_dir/input/01_10x_v3_pbmc1k \\\n--sample=pbmc_1k_v3 \\\n--expect-cells=1000 \\\n--nosecondary\n\n### id = output folder name\n### transcriptome = reference folder name\n### fastqs = input folder\n### sample = prifix of input file name\n```\n#### Example\npbmc1k_cellranger_matrix.mtx.gz / \npbmc1k_cellranger_features.tsv.gz / \npbmc1k_cellranger_barcodes.tsv.gz\n\n### 2-2. CellRanger to SeaShell_Analyzer data -> output = 'S01_preprocessed.rds'\n```\n### copy 'matrix.mtx.gz', 'features.tsv.gz', 'barcodes.tsv.gz', and 'web_summary.html' to ./my_dir/output\ndocker cp seashell:/output_folder1/outs/filtered_feature_bc_matrix/matrix.mtx.gz ./my_dir/output\ndocker cp seashell:/output_folder1/outs/filtered_feature_bc_matrix/features.tsv.gz ./my_dir/output\ndocker cp seashell:/output_folder1/outs/filtered_feature_bc_matrix/barcodes.tsv.gz ./my_dir/output\ndocker cp seashell:/output_folder1/outs/web_summary.html ./my_dir/output\n\n### Generate 'S01_preprocessed.rds'\ndocker exec seashell Rscript /home/script/ToSeashell.R -d /home/my_dir/output -t cellranger\n```\n#### Example\nS01_preprocessed.rds (pbmc1k_cellranger2seashell.rds)\n\n### 2-3. zUMIs 2.9.4 -> output = 'BD_Rhapsody.dgecounts.rds', 'BD_Rhapsody.readcount.exon.all.loom' and 'BD_Rhapsody.detected_cells.pdf'\n```\n### create zUMIs_used.yaml\ndocker exec seashell python3 /home/script/config_editor.py \\\n-o /home/my_dir/output \\\n-f /home/my_dir/input/02_BD_wholeblood/SRR14702879_1.fastq.gz \\\n-q /home/my_dir/input/02_BD_wholeblood/SRR14702879_2.fastq.gz \\\n-r /home/my_dir/ref/zumis_ref/hg38 \\\n-p BD -s hs -t 12\n\n### Run zUMIs\ndocker exec seashell /home/apps/zUMIs/zUMIs.sh -c -y /home/my_dir/output/zUMIs_used.yaml\n```\n\n### 2-4. zUMIs to SeaShell_Analyzer data -> output = 'S01_preprocessed.rds'\n```\n### copy 'BD_Rhapsody.dgecounts.rds' to ./my_dir/output\ncp ./my_dir/output/zUMIs_output/expression/BD_Rhapsody.dgecounts.rds ./my_dir/output\n\n### If you want to see 'BD_Rhapsody.readcount.exon.all.loom' and 'BD_Rhapsody.detected_cells.pdf'\ncp ./my_dir/output/zUMIs_output/expression/BD_Rhapsody.readcount.exon.all.loom ./my_dir/output\ncp ./my_dir/output/zUMIs_output/stats/BD_Rhapsody.detected_cells.pdf ./my_dir/output\n\n### Generate 'S01_preprocessed.rds'\ndocker exec seashell Rscript /home/script/ToSeashell.R -d /home/my_dir/output -t zUMIs\n```\n\n### 2-5. Csv or Loom to SeaShell_Analyzer data -> output = 'S01_preprocessed.rds'\n```\n### copy your csv or loom file to ./my_dir/output\n#### csv file\n docker exec seashell Rscript /home/script/ToSeashell.R -d /home/my_dir/output -t csv\n#### loom file\n docker exec seashell Rscript /home/script/ToSeashell.R -d /home/my_dir/output -t loom\n```\n\n## 3. Run SeaShell_Data by galaxy mode\n```\n### Start galaxy server\ndocker exec seashell sh /root/galaxy/run.sh &\n\n### Open the galaxy in the browser. Account/Password = seashell@galaxy.org/seashell@2021\nhttp://Your_IP_Address:8080/\n```\n### 3-0. Upload files\n

\n### 3-1. CellRanger 3.0.2 -> output = 'matrix.mtx.gz', 'features.tsv.gz', 'barcodes.tsv.gz', and 'web_summary.html'\n

\n\n### 3-2. CellRanger to SeaShell_Analyzer data -> output = 'S01_preprocessed.rds'\n

\n\n### 3-3. zUMIs 2.9.4 -> output = 'BD_Rhapsody.dgecounts.rds', 'BD_Rhapsody.readcount.exon.all.loom' and 'BD_Rhapsody.detected_cells.pdf'\n\n### 3-4. zUMIs to SeaShell_Analyzer data -> output = 'S01_preprocessed.rds'\n\n### 3-5. Csv or Loom to SeaShell_Analyzer data-> output = 'S01_preprocessed.rds'\n\n## 4. Use Seashell_Analyzer\n```\n### Start Shiny server\ndocker exec seashell nohup shiny-server & \n\n### Open the Seashell in the browser. \nhttp://Your_IP_Address:8081/seashell/\n```\n\n## 5. Stop service\n```\n### remove seashell container\ndocker rm -f seashell\n\n```\n\n# Current problems\n1. If the website is not active for a period of time, it will be automatically back to the home page. \n2. Only **UMAP** can be used in the clustering module.","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",14083755572,"orgData","recentTags",[87],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":96,"_46":113,"_114":90,"_115":29,"_116":52,"_53":117,"_118":119,"_120":104,"_121":113,"_122":62,"_123":17},"content_type","creator",1840387,"full_size",7028616122,"id",155861839,"images",[97],{"_98":99,"_100":101,"_102":44,"_103":104,"_105":106,"_107":108,"_109":44,"_110":-5,"_111":92,"_59":62,"_112":-5},"architecture","amd64","digest","sha256:fc631b03e795ce6e8aa66e7f8ef4f4bf22c373c8e9f38d89f7961526eedb45e9","features","last_pulled","2026-09-11T15:54:38.017050518Z","last_pushed","2022-01-12T09:42:47Z","os","linux","os_features","os_version","size","variant","2022-01-12T09:42:46.860641Z","last_updater","last_updater_username","media_type","latest","repository",14766082,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":133,"_140":141,"_129":150,"_151":11},{"_36":134,"_38":135,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":136,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":137,"_75":11,"_76":139,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":138},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_142":60,"_143":-5,"_144":-5,"_145":146},"count","next","previous","results",[147],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":148,"_46":113,"_114":90,"_115":29,"_116":52,"_53":117,"_118":119,"_120":104,"_121":113,"_122":62,"_123":17},[149],{"_98":99,"_100":101,"_102":44,"_103":104,"_105":106,"_107":108,"_109":44,"_110":-5,"_111":92,"_59":62,"_112":-5},[],"canDeleteTags","actionData","errors"]

lsbnb/seashell

Tags for lsbnb/seashell