Deploy FLY CELL ATLAS database by SeuratExplorer Server

why do this?

As a step-by-step tutorial to guides users build their own scRNAseq database by R package - SeuratExplorerServer, which also provide researchers a new tool to investigate fly scRNAseq data.

Check the demo database

1. prepare data

Download data from FLY CELL ATLAS, only select H5AD files.

method 1

use specific download managers, such as Neat Download Manager (for windows) or Uget (for linux).

method 2

too slow, not recommended!

sh download_data.sh

the organized directory:

Data
├── Antenna
│ ├── 10×
│ │ └── s_fca_biohub_antenna_10x.h5ad
│ └── Smart-seq2
│     └── antenna.h5ad
├── Body
│ └── 10×
│     └── s_fca_biohub_body_10x.h5ad
├── Bodywall
│ ├── 10×
│ │ └── s_fca_biohub_body_wall_10x.h5ad
│ └── Smart-seq2
│     └── body_wall.h5ad
├── Fatbody
│ ├── 10×
│ │ └── s_fca_biohub_fat_body_10x.h5ad
│ └── Smart-seq2
│     └── fat_body.h5ad
.......................................
└── Wing
    ├── 10×
    │ └── s_fca_biohub_wing_10x.h5ad
    └── Smart-seq2
        └── wing.h5ad

49 directories, 32 files

2. Trans python anndata object to R Seurat object

s2.1_trans-anndata-to-seurat.sh: install related packages

s2.2_update-anndata-to-use-raw.ipynb: to use raw if anndata has raw, for usually raw has more genes

s2.3_trans-anndata-to-seurat.R: use R package - schard to tran anndata object to seurat object

3. Build scRNAseq database

3.1 prepare directory

Build directories bellow, which should under shinyserver site direcotry, refer to 'Database Deployment Guide' part from fentouxungui/SeuratExplorerServer

shiny-server/
├── apps
└── index-page

apps to save individual app for each tissue index-page to browse all apps, which has included all urls of all apps

3.2 generate credentials file

s3.1_generate-credentials-file.R: to create a credentials file

after create credentials, modify the credentials parameter in app.R_demo file.

3.3 batch create apps

s3.2_batch-generate-apps.R: batch create apps for each tissue

now you can test each app by use url: IP address plus app directory

in the demo: http://www.nibs.ac.cn:666 is the shiny-server IP address (with port), FlyCellAtlas-SES/shiny-server/apps/Antenna/ is the relative path to shiny-server site directory. The demo shiny-server site directory is set to /home/zhangyc/ShinyServer.

3.4 build index page

app.R_index.R : modify IP_address, relative_path, downloaded_data_info_file. then put it into index-page directory, and remame it to app.R. This app is just for demo, you can make this app multifunctional in fact.

now you can visit index page use url: IP address plus index app directory

in the demo: http://www.nibs.ac.cn:666 is the shiny-server IP address (with port), FlyCellAtlas-SES/shiny-server/index-page/ is the relative path to shiny-server site directory. The demo shiny-server site directory is set to /home/zhangyc/ShinyServer.

Data and codes availability

all data and scripts can be downloaded from Fly Cell Atlas - by SeuratExplorer Server, and the scripts can also be downloaded from github - fentouxungui/FlyCellAtlas-SES

Congratulations!