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zqfang committed Dec 8, 2022
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60 changes: 30 additions & 30 deletions docs/gseapy_example.ipynb
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}
},
"source": [
"## 1. Biomart API \n",
"## Biomart API \n",
"\n",
"Don't use this if you don't know Biomart\n",
"\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 1.1 convert gene identifiers"
"### Convert gene identifiers"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 1.2 Mouse gene symbols maps to Human, or Vice Versa\n",
"### Mouse gene symbols maps to Human, or Vice Versa\n",
"\n",
"This is useful when you have troubles to convert gene symbols between human and mouse"
]
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 1.3 Gene Symbols Conversion for the GMT file\n",
"### Gene Symbols Conversion for the GMT file\n",
"This is useful when runing GSEA for non-human species\n",
"\n",
"**e.g. Convert Human gene symbols to Mouse.**"
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}
},
"source": [
"## 2. Enrichr API"
"## Enrichr API"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.1 Over-representation analysis by Enrichr web services\n",
"### Over-representation analysis by Enrichr web services\n",
"\n",
"The only requirement of input is a list of gene symbols.\n",
"\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.2 Over-representation analysis via Enrichr web services\n",
"### Over-representation analysis via Enrichr web services\n",
"\n",
"This is an Example of the Enrichr analysis\n",
"\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.3 Over-representation analysis (hypergeometric test) by offline\n",
"### Over-representation analysis (hypergeometric test) by offline\n",
"\n",
"This API **DO NOT** use Enrichr web services.\n",
"\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 2.4 Plotting"
"### Plotting"
]
},
{
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}
},
"source": [
"### 2.5 Command line usage "
"### Command line usage "
]
},
{
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}
},
"source": [
"## 3. Prerank example\n",
"## Prerank example\n",
"\n",
"### 3.1 Assign prerank() with \n",
"### Assign prerank() with \n",
"\n",
"- pd.DataFrame: Only contains two columns, or one cloumn with gene_name indexed \n",
"- pd.Series \n",
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" - Do not include header in your gene list ! \n",
"\n",
"\n",
"### NOTE: UPCASES for gene symbols by Default\n",
"#### NOTE: UPCASES for gene symbols by Default\n",
"\n",
"1. Gene symbols are all \"UPCASES\" in the Enrichr Libaries. You should convert your input gene identifier to \"UPCASES\" first.\n",
"2. If input `gmt`, `dict` object, please refer to `1.2 Mouse gene symbols maps to Human, or Vice Versa` (in this page) to convert gene identifier\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 3.2 How to generate your GSEA plot inside python console \n",
"### How to generate your GSEA plot inside python console \n",
"Visualize it using ``gseaplot`` \n",
"\n",
"Make sure that ``ofname`` is not None, if you want to save your figure to the disk"
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}
},
"source": [
"### 3.2 Command line usage "
"### Command line usage "
]
},
{
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}
},
"source": [
"## 4. GSEA Example\n",
"## GSEA Example\n",
"\n",
"\n",
"### 4.1 Inputs \n",
"### Inputs \n",
"\n",
"Assign gsea() \n",
"\n",
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"```\n",
"\n",
"\n",
"### NOTE: UPCASES for gene symbols by Default\n",
"#### NOTE: UPCASES for gene symbols by Default\n",
"\n",
"1. Gene symbols are all \"UPCASES\" in the Enrichr Libaries. You should convert your input gene identifier to \"UPCASES\" first.\n",
"2. If input `gmt`, `dict` object, please refer to `1.2 Mouse gene symbols maps to Human, or Vice Versa` (in this page) to convert gene identifier\n"
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 4.2 Show the gsea plots\n",
"### Show the gsea plots\n",
"\n",
"The **gsea** module will generate heatmap for genes in each gene sets in the backgroud. \n",
"But if you need to do it yourself, use the code below"
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}
},
"source": [
"### 4.3 Command line usage "
"### Command line usage "
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"## 5. Single Sample GSEA example\n",
"## Single Sample GSEA example\n",
"\n",
"**Note: When you run ssGSEA, all genes names in your gene_sets file should be found in your expression table**\n",
"\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 5.1 Input format \n",
"#### Input format \n",
"Assign \n",
"- `data` with \n",
" - a txt file, gct file, \n",
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"```\n",
"\n",
"\n",
"### NOTE: UPCASES for gene symbols by Default\n",
"#### NOTE: UPCASES for gene symbols by Default\n",
"\n",
"1. Gene symbols are all \"UPCASES\" in the Enrichr Libaries. You should convert your input gene identifier to \"UPCASES\" first.\n",
"2. If input `gmt`, `dict` object, please refer to `1.2 Mouse gene symbols maps to Human, or Vice Versa` (in this page) to convert gene identifier\n"
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 5.2 Access Enrichment Score (ES) and NES\n",
"### Access Enrichment Score (ES) and NES\n",
"\n",
"results are saved to obj.res2d"
"Results are saved to obj.res2d"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 5.3 command line usage of single sample gsea"
"### Command line usage of ssGSEA"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"## 6. Replot Example\n",
"## Replot Example\n",
"\n",
"### 6.1 locate your directory\n",
"### Locate your directory\n",
"\n",
"notes: ``replot`` module need to find edb folder to work properly.\n",
"Notes: ``replot`` module need to find edb folder to work properly.\n",
"keep the file tree like this:\n",
"```\n",
"data\n",
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 6.2 command line usage of replot"
"### Command line usage of replot"
]
},
{
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10 changes: 5 additions & 5 deletions docs/singlecell_example.ipynb
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 1. Read Demo Data"
"### Read Demo Data"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 2. GSEA "
"### GSEA"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 3. DEG Analysis"
"### DEG Analysis"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 4. Over-representation analysis (Enrichr API)"
"### Over-representation analysis (Enrichr API)"
]
},
{
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"cell_type": "markdown",
"metadata": {},
"source": [
"### 5. Network Visualization"
"### Network Visualization"
]
},
{
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