Ssgsea Immune Infiltration Analysis

OrganizationPopular

aipoch

ssgsea-immune-infiltration-analysis

Use when estimating immune infiltration from bulk RNA-seq expression matrices with ssGSEA/GSVA, comparing case versus control groups, and generating downstream immune-score visualizations. NOT for single-cell RNA-seq, absolute cell proportion estimation, or clinical decision making.

Overview

Publisher	aipoch
Repository	`medical-research-skills`
Skill name	`ssgsea-immune-infiltration-analysis`
Stars	1.9K
Forks	175
Bundled files	16
License	MIT
Links	Skill source Repository Homepage

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
16 bundled files
Scripts, templates, and references the model can read while it works. Files are read-only and never executed.
Open source
Published by aipoch on GitHub. Read the source before you install it.

Installation

Install the Ssgsea Immune Infiltration Analysis AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
Enable the skill in any chat where you want it available.

Store

Installed

Skills

Add skills

Import one or more skills from a public GitHub folder or a local .skill or .zip archive, or SKILL.md file.

From GitHub URLFrom .skill, .zip, or SKILL.md

GitHub repo or folder

https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/ssgsea-immune-infiltration-analysis

Points to a single skill folder, or any folder that contains multiple skills. Public repos only.

CancelContinue

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Use it in TypingMind

Enable Ssgsea Immune Infiltration Analysis in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Ssgsea Immune Infiltration Analysis on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Ssgsea Immune Infiltration Analysis is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

Source: https://github.com/aipoch/medical-research-skills

ssGSEA Immune Infiltration Analysis

When to Use

Estimate relative immune infiltration from a bulk RNA-seq expression matrix.
Compare immune enrichment scores between one case group and one control group.
Generate structured result tables plus optional PDF visualizations for downstream review.

When Not to Use

Single-cell RNA-seq or spatial transcriptomics.
Absolute immune cell proportion estimation or deconvolution.
Clinical diagnosis, treatment recommendation, or any other medical decision making.

Workflow

Confirm that the expression matrix, group file, and gene-set file match the documented schemas.
Run scripts/main.R with the target case and control groups.
Review run_record.txt, output_manifest.txt, and the generated tables or plots.
If execution fails, read references/troubleshooting.md before retrying.

When to Read External Files

Situation	File to Read	Purpose
Need to run the analysis	`scripts/main.R`	CLI entry point
Need algorithm details	`references/algorithm.md`	Method assumptions and interpretation
Encounter an error	`references/troubleshooting.md`	Error codes and fixes
Need CLI examples or baseline execution details	`references/cli-guide.md`	Examples and recorded run details
Need dependency declarations	`DESCRIPTION`	Package list and Bioconductor source note
Need test commands	`tests/run_tests.R`	End-to-end test entry

Usage

bash
Rscript scripts/main.R \
  --input_file ./expression_matrix.csv \
  --group_file ./group_info.csv \
  --gene_set ./immune_gene_sets.csv \
  --case_group treatment \
  --control_group control \
  --output_dir ./output \
  --method ssgsea \
  --seed 42

Validated path note:

ssgsea is the default validated path.
gsva is supported, but only with kernels validated in the local GSVA environment.
In the current audited environment, gsva with Gaussian completed successfully and is the documented baseline.

Arguments

Short	Long	Type	Default	Description
`-i`	`--input_file`	file	required	Expression matrix with genes as rows and samples as columns
`-g`	`--group_file`	file	required	Group annotation table
`-e`	`--gene_set`	file	`tests/data/immune_gene_sets.csv`	Immune gene-set CSV
`-a`	`--case_group`	string	required	Case group label
`-b`	`--control_group`	string	required	Control group label
`-o`	`--output_dir`	dir	`./output`	Output directory
`-m`	`--method`	string	`ssgsea`	GSVA method: `ssgsea`, `gsva`
`-k`	`--kcdf`	string	`Gaussian`	Kernel mode: `Gaussian`, `Poisson`; `Gaussian` is the validated GSVA baseline
`-n`	`--min_sz`	integer	`2`	Minimum overlap genes per gene set
`-x`	`--max_sz`	integer	`10000`	Maximum genes per gene set
`-p`	`--parallel_sz`	integer	`2`	Requested parallel CPU count
`-u`	`--tau`	numeric	`0.25`	Tau parameter for ssGSEA
`-d`	`--mx_diff`	boolean	`true`	GSVA `mx.diff` switch
`-c`	`--gene_id_case`	string	`upper`	Gene ID normalization: `asis`, `upper`, `lower`
`-s`	`--seed`	integer	`42`	Random seed
`-t`	`--timeout_seconds`	integer	`0`	Optional timeout; `0` disables it
	`--sample_col`	string/int	none	Sample column name or 1-based index
	`--group_col`	string/int	none	Group column name or 1-based index
	`--make_plots`	boolean	`true`	Generate PDF plots
	`--verbose`	boolean	`true`	Print progress logs

Input Format

Expression Matrix

CSV or TSV. The first column must contain gene identifiers. Remaining columns are sample-level numeric expression values.

csv
gene,Sample1,Sample2,Sample3
TP53,10.2,8.5,9.1
CXCL9,4.3,6.1,5.7

Group File

CSV or TSV with at least one sample column and one group column.

csv
sample,group
Sample1,control
Sample2,treatment
Sample3,treatment

Gene Set File

CSV with gene and cell_type; immunity_class is optional.

csv
gene,cell_type,immunity_class
CXCL9,Activated CD8 T cell,Adaptive
CD3D,Activated CD8 T cell,Adaptive

Output Files

File	Description
`data/ssgsea_list.rds`	Serialized analysis result object
`table/ssgsea_scores_long.csv`	Long-format immune infiltration scores
`table/ssgsea_scores_wide.csv`	Wide-format immune infiltration score matrix
`table/ssgsea_group_compare.csv`	Case-vs-control comparison summary
`table/immune_cell_correlation_matrix.csv`	Immune-cell Spearman correlation matrix
`table/immune_cell_correlation_pvalue.csv`	Correlation p-value matrix
`plot/immune_cell_composition_sample.pdf`	Sample-level composition plot; generated only when `--make_plots=true`
`plot/immune_group_boxplot.pdf`	Group comparison boxplot; generated only when `--make_plots=true`
`plot/immune_correlation_heatmap.pdf`	Immune-cell correlation heatmap; generated only when `--make_plots=true`
`plot/gene_immune_correlation_scatter_*.pdf`	Auto-selected gene-vs-cell scatter plot; generated only when `--make_plots=true`
`run_record.txt`	Structured execution record
`output_manifest.txt`	Output file manifest with descriptions
`session_info.txt`	R session information

Error Handling

Error	Cause	Solution
`SKILL_FILE_NOT_FOUND`	Input file path is invalid	Check file paths
`SKILL_MISSING_COLUMNS`	Required columns are absent	Fix the input schema
`SKILL_EMPTY_DATA`	No usable rows, gene sets, or aligned samples remain	Check IDs and filters
`SKILL_INVALID_PARAMETER`	CLI value is invalid or data is malformed	Review arguments and file content
`SKILL_SAMPLE_MISMATCH`	Expression and group samples do not align	Harmonize sample identifiers
`SKILL_PACKAGE_NOT_FOUND`	Required R package is missing	Install the missing package
`SKILL_TIMEOUT`	The configured time limit was exceeded	Increase `--timeout_seconds` or disable it with `0`

Testing

bash
Rscript scripts/main.R --help

Rscript tests/run_tests.R

Rscript tests/test_skill.R

tests/test_skill.R is self-contained: if expected outputs are absent, it first runs tests/run_tests.R and then validates both file presence and core result structure.

Bundled files

The model reads these on demand while the skill is loaded. They are exposed as readable files and are never executed.

eval_report_ssgsea-immune-infiltration-analysis_result.json13 KB
references/algorithm.md1 KB
references/cli-guide.md7 KB
references/troubleshooting.md2 KB
scripts/cli_options.R4 KB
scripts/functions.R4 KB
scripts/io.R5 KB
scripts/main.R2 KB
scripts/recording.R1 KB
scripts/run_analysis.R8 KB
scripts/utils.R3 KB
scripts/visualization.R4 KB
tests/data/expression_matrix.csv24.9K KB
tests/data/group_info.csv3 KB
tests/data/immune_gene_sets.csv28 KB
tests/run_tests.R4 KB

Frequently asked questions

What does the Ssgsea Immune Infiltration Analysis AI skill do?

Why use Ssgsea Immune Infiltration Analysis on TypingMind?

Because you install it once and use it with any model. Ssgsea Immune Infiltration Analysis is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Ssgsea Immune Infiltration Analysis in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/aipoch/medical-research-skills/tree/main/awesome-med-research-skills/Data%20Analysis/ssgsea-immune-infiltration-analysis. TypingMind reads its SKILL.md and bundles its files and installs it as a skill you can enable per chat.

Which AI models can use Ssgsea Immune Infiltration Analysis?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Ssgsea Immune Infiltration Analysis?

As many as you like. As long as a model supports skills, you can use Ssgsea Immune Infiltration Analysis with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Ssgsea Immune Infiltration Analysis AI skill free?

Yes. It is published on GitHub by aipoch under the MIT license. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Use it in TypingMind

Works with any AI model

Skill instructions

ssGSEA Immune Infiltration Analysis

When to Use

When Not to Use

Workflow

When to Read External Files

Usage

Arguments

Input Format

Expression Matrix

Group File

Gene Set File

Output Files

Error Handling

Testing

Bundled files

Frequently asked questions

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