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07-HemaScopeCloud_Tutorial.Rmd
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07-HemaScopeCloud_Tutorial.Rmd
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---
editor_options:
markdown:
wrap: 72
---
# Operation Manual for the HemaScopeCloud
## User Login
### Enter the URL in a web browser:
[*https://hemascope.hiplot.cn/?home=hemascope*](https://hemascope.hiplot.cn/?home=hemascope)
and click to access the login page.
```{r echo=FALSE,fig.cap="Login Page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/loginpage.png")
```
### To obtain free computational resources:
Enter your login email, click "Get Code," input the verification code
received in your email, and then click "Login" to complete the login and
access the system homepage.
### To browse HemaScopeCloud without needing computational resources:
Click the "View without Login" button to access the system homepage. You
can view demo analysis projects. If you click the button to initiate an
analysis, the platform will prompt: "Please log in for analysis!"
## Homepage
```{r echo=FALSE,fig.cap="Homepage", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/homepage.png")
```
The left side features a menu bar containing Home, Data, Analysis,
Project, and Help. And the upper right section includes statistics on
analysis project status, usage of analysis projects, a quick entry for
creating new analysis projects, and statistics on allocated storage
capacity usage.
**Statistics on Analysis Project Status**
**Pending Analysis：**Waiting for analysis, not yet submitted for
analysis.
**Pending Resources：**Waiting for resources, analysis submitted and
awaiting resource allocation.
**Analyzing：**Currently analyzing.
**Completed：**Analysis completed.
**Error：**An error occurred during analysis.
**Total：**Total of all analysis statuses.
**Usage Statistics for Analysis Projects:** Number of used analysis
projects / Total number of allocated analysis projects. The current
allocation for the system is 50 projects. For additional free
computational resources, please contact the developer.
**Quick Entry for Creating New Analysis Projects:** Supports quick
access to the new analysis project pages corresponding to two pipelines.
**Storage Capacity Usage:** Used Storage Resources / Allocated Storage
Resources.
The lower section displays the most recently run analysis projects. By
default, it shows demo projects upon initial entry. Clicking the "View"
option on an entry in the Projects section allows you to access and
analyze that specific analysis project.
## Data Page
The Data page includes storage for Demo sample project data as well as
Personal project data. Data under the Demo tab can be downloaded, while
the Personal tab allows users to create new folders and upload files.
## Analysis Page
It lists two analysis pipelines: sc_HemaScopeCloud and
st_HemaScopeCloud, serving as entries for creating new analysis
projects. Click the Analysis button to access the new project and
execution page for that pipeline.
```{r echo=FALSE,fig.cap="Select Analysis Pipeline Page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/SelectAnalysisPipelinePage.png")
```
```{r echo=FALSE,fig.cap="Enter the Analysis Pipeline Page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/EntertheAnalysisPipelinePage.png")
```
**Create New Analysis Project**
Click the Analysis button under the sc_HemaScopeCloud to enter the new
project page for that pipeline.
**Project Name：**Enter the name of the analysis project for
identification purposes.
**Input Data：**Click Upload to upload local analysis files. Single and
multiple file uploads are supported. Uploaded files must comply with the
pipeline's input file requirements; otherwise, an error will occur
during execution.
**Sample Name：**Click Add to enter the sample names, which should
correspond to the uploaded analysis files.
Items marked with \* are required fields.
**Click the Run button to initiate the analysis：**For the scRNA-seq
pipeline，this will trigger step1-4; for the st-seq pipeline, it will
trigger step1-5.
Each subsequent analysis step requires clicking Run on the relevant step
page to submit. Before submission, ensure that the previous step has
generated result files; otherwise, a notification will indicate that the
analysis cannot proceed.
**Load Demo Data**
HemaScopeCloud supports loading pre-configured analysis demo files and
default parameters to quickly initiate analysis projects. On the new
project page, click Load Demo Data to load files from the demo project
and fill the required fields. Then, click the Run button to execute the
analysis for the demo project.
```{r echo=FALSE,fig.cap="Load Demo Data", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/LoadDemoData.png")
```
After clicking Run, you will be redirected to the detailed page of the
analysis project.
**Analysis Project Detail Page Notifications**
**Waiting for resources...Do not submit repeatedly:** This indicates
that the submission is waiting for resources. Do not click the Run
button again.
**Analyzing...Do not submit repeatedly:** This indicates that the
project is currently analyzing. Do not click the Run button again.
**Analysis Steps, Current Analysis Step:** Displays all stepwise
analysis processes and the current step. Click on different steps to
navigate to the corresponding analysis step page. For the initial
analysis, you must complete the previous step before proceeding to the
next one.
**Refresh Button:** Used to refresh the current page.
**Results:** This tab stores the results of the completed step.
**Visualization:** For steps that involve visualizations, the results
will be found under the visualization tab.
**History：**Click on Run History to view all historical runs of that
step.
**Status：**Corresponds to the analysis status of the project.
**Log：**Click this button to view the run log.
**Parameter Settings：**Used for entering parameter values.
```{r echo=FALSE,fig.cap="Analysis Project Page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/AnalysisProjectPage.png")
```
```{r echo=FALSE,fig.cap="Analysis Project Result Page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/AnalysisProjectResultPage.png")
```
```{r echo=FALSE,fig.cap="This step of the analysis project displays 'Waiting for resources…Do not submit repeatedlly'", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/Thisstepoftheanalysisprojectdisplays.png")
```
```{r echo=FALSE,fig.cap="This step of the analysis project displays 'Analyzing…Do not submit repeatedly'", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/ThisstepoftheanalysisprojectdisplaysAnalyzing.png")
```
```{r echo=FALSE,fig.cap="History Page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/HistoryPage.png")
```
**Note:** For steps that have already been completed (except for the
first step), you can adjust the parameters and click Run to perform
multiple analyses. The results page will retain only the latest analysis
results.
## Projects page
The homege includes analysis projects created by the user as well as
pre-configured demo analysis projects provided by the system.
```{r echo=FALSE,fig.cap="Demo projects and user’s personal projects", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/Demoprojectsanduserspersonalprojects.png")
```
Clicking "View" allows you to navigate to the analysis project for
review and step-by-step analysis.
```{r echo=FALSE,fig.cap="Click 'View' to access the analysis project", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/ClickViewtoaccesstheanalysisproject.png")
```
```{r echo=FALSE,fig.cap="Enter the detailed analysis project page", out.width = "800px" , fig.align = 'center'}
knitr::include_graphics(path="./image/hemascopecloud/Enterthedetailedanalysisprojectpage.png")
```