sc-count

Default scRNA counting route. Turn FASTQ or existing Cell Ranger, STARsolo, SimpleAF / Alevin-fry, or kb-python outputs into a downstream-ready standardized AnnData.

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Repository: mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Last source activity: April 30, 2026 at 21:29
Detected SKILL.md language: English
Stars: 31
Forks: 8

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🧬 Single-Cell Counting

You are SC Count, a specialized OmicsClaw agent for converting scRNA-seq FASTQ input into standardized count matrices and a downstream-ready AnnData.

Why This Exists

Without it: users must run Cell Ranger or STARsolo manually, then convert outputs again before starting OmicsClaw downstream skills.

With it: one wrapper produces a standardized h5ad, basic count QC figures, and preserves backend artifacts.

Why OmicsClaw: it narrows the public surface to mainstream 10x-oriented inputs while wiring the result directly into the existing AnnData-first single-cell workflow.

Core Capabilities

Four counting backends: Cell Ranger, STARsolo, SimpleAF / Alevin-fry, and kb-python.

Direct import path: can also standardize existing backend output directories without rerunning them.

Stable downstream contract: writes processed.h5ad with layers['counts'] and OmicsClaw input-contract metadata.

Standard output layer: barcode-rank and count-distribution figures plus machine-readable tables.

Reproducibility layer: writes README.md, report.md, result.json, and rerun commands.

Input Formats

Format

Extension

Required Fields / Structure

Example

FASTQ directory

directory

one or more 10x-style FASTQs, optionally multiple samples

fastqs/

FASTQ file

.fastq.gz

one mate file plus --read2 for paired input

PBMC_R1.fastq.gz

Cell Ranger output

directory

contains outs/filtered_feature_bc_matrix*

sample_count/

STARsolo output

directory

contains Solo.out/Gene/filtered/

starsolo_pbmc/

Demo

n/a

--demo flag

🧬 Single-Cell Counting

You are SC Count, a specialized OmicsClaw agent for converting scRNA-seq FASTQ input into standardized count matrices and a downstream-ready AnnData.

Why This Exists

Without it: users must run Cell Ranger or STARsolo manually, then convert outputs again before starting OmicsClaw downstream skills.

With it: one wrapper produces a standardized h5ad, basic count QC figures, and preserves backend artifacts.

Why OmicsClaw: it narrows the public surface to mainstream 10x-oriented inputs while wiring the result directly into the existing AnnData-first single-cell workflow.

Core Capabilities

Four counting backends: Cell Ranger, STARsolo, SimpleAF / Alevin-fry, and kb-python.

Direct import path: can also standardize existing backend output directories without rerunning them.

Stable downstream contract: writes processed.h5ad with layers['counts'] and OmicsClaw input-contract metadata.

Standard output layer: barcode-rank and count-distribution figures plus machine-readable tables.

Reproducibility layer: writes README.md, report.md, result.json, and rerun commands.

Input Formats

Format

Extension

Required Fields / Structure

Example

FASTQ directory

directory

one or more 10x-style FASTQs, optionally multiple samples

fastqs/

FASTQ file

.fastq.gz

one mate file plus --read2 for paired input

PBMC_R1.fastq.gz

Cell Ranger output

directory

contains outs/filtered_feature_bc_matrix*

sample_count/

STARsolo output

directory

contains Solo.out/Gene/filtered/

starsolo_pbmc/

Demo

n/a

--demo flag

name	sc-count
description	Default scRNA counting route. Turn FASTQ or existing Cell Ranger, STARsolo, SimpleAF / Alevin-fry, or kb-python outputs into a downstream-ready standardized AnnData.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["singlecell","scrna","count","cellranger","starsolo","simpleaf","kb-python","fastq"]
metadata	{"omicsclaw":{"domain":"singlecell","requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"🧬","homepage":"https://github.com/TianGzlab/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["Cell Ranger count","STARsolo count","fastq to adata","raw single-cell counting","generate count matrix"],"allowed_extra_flags":["--chemistry","--method","--read2","--reference","--sample","--t2g","--threads","--whitelist","--r-enhanced"],"legacy_aliases":["scrna-count","sc-pseudoalign-count","scrna-pseudoalign-count"],"saves_h5ad":true,"requires_preprocessed":false,"param_hints":{"cellranger":"[Truncated]","starsolo":"[Truncated]","simpleaf":"[Truncated]","kb_python":"[Truncated]"}}}

name	sc-count
description	Default scRNA counting route. Turn FASTQ or existing Cell Ranger, STARsolo, SimpleAF / Alevin-fry, or kb-python outputs into a downstream-ready standardized AnnData.
version	0.1.0
author	OmicsClaw
license	MIT
tags	["singlecell","scrna","count","cellranger","starsolo","simpleaf","kb-python","fastq"]
metadata	{"omicsclaw":{"domain":"singlecell","requires":{"bins":"[Truncated]","env":"[Truncated]","config":"[Truncated]"},"emoji":"🧬","homepage":"https://github.com/TianGzlab/OmicsClaw","os":["macos","linux"],"install":["[Truncated]"],"trigger_keywords":["Cell Ranger count","STARsolo count","fastq to adata","raw single-cell counting","generate count matrix"],"allowed_extra_flags":["--chemistry","--method","--read2","--reference","--sample","--t2g","--threads","--whitelist","--r-enhanced"],"legacy_aliases":["scrna-count","sc-pseudoalign-count","scrna-pseudoalign-count"],"saves_h5ad":true,"requires_preprocessed":false,"param_hints":{"cellranger":"[Truncated]","starsolo":"[Truncated]","simpleaf":"[Truncated]","kb_python":"[Truncated]"}}}

Requirement	Where it should exist	Why it matters
Raw FASTQs or existing count output	input path	counting requires raw reads or a backend output directory to import
Backend reference	`--reference`	required for real backend runs
10x chemistry contract	`--chemistry`, `--whitelist`	required for STARsolo barcode/UMI parsing
Transcript-to-gene map	`--t2g`	required for kb-python runs

Parameter	Default	Description
`--method`	`cellranger`	choose Cell Ranger, STARsolo, SimpleAF / Alevin-fry, or kb-python
`--reference`	none	backend reference directory or index path
`--t2g`	none	transcript-to-gene map for kb-python
`--sample`	none	choose one sample from a multi-sample FASTQ directory
`--threads`	`8`	thread count for backend execution
`--chemistry`	`auto`	Cell Ranger auto-detects; STARsolo requires explicit supported chemistry
`--whitelist`	none	STARsolo barcode whitelist file

Flag	Type	Default	Description	Validation
`--input`	str	None	FASTQ path or existing Cell Ranger / STARsolo output directory	Required unless `--demo`
`--output`	str	—	Output directory	Required
`--demo`	flag	off	Run with built-in demo data	—
`--method`	str	`cellranger`	Counting backend	Choices: `cellranger`, `starsolo`, `simpleaf`, `kb_python`
`--reference`	str	None	Backend reference path (Cell Ranger transcriptome, STAR genome dir, simpleaf index, or kallisto index)	Required for real backend runs
`--t2g`	str	None	Transcript-to-gene map for kb-python runs	Required for `kb_python` method
`--sample`	str	None	Choose one sample from a multi-sample FASTQ directory	—
`--read2`	str	None	Explicit mate FASTQ when `--input` points to one file	—
`--threads`	int	8	Backend thread count	—
`--chemistry`	str	`auto`	Chemistry hint; STARsolo supports `10xv2`, `10xv3`, `10xv4`; Cell Ranger auto-detects	—
`--whitelist`	str	None	STARsolo barcode whitelist file	Strongly recommended for STARsolo real runs
`--r-enhanced`	flag	off	Accepted for CLI consistency; no R Enhanced plots for this skill	No-op

sc-count

Install options

Review the source files

🧬 Single-Cell Counting

Why This Exists

Core Capabilities

Input Formats

🧬 Single-Cell Counting

Why This Exists

Core Capabilities

Input Formats

Data / State Requirements

Beginner Setup Hint

Workflow

CLI Reference

Example Queries

Algorithm / Methodology

Cell Ranger Path

STARsolo Path

SimpleAF / Alevin-fry Path

kb-python Path

Visualization Contract

Output Structure

Reproducibility Contract

Knowledge Companions

Dependencies

Environment Management

CLI Parameters

R Enhanced Plots

Special Requirements

Reference Files

Direct Import (No Re-run)

Workflow Position

Backend	`--reference` points to	Also needs
`cellranger`	Cell Ranger transcriptome dir (e.g., `refdata-gex-GRCh38-2020-A`)	—
`starsolo`	STAR genome directory (built from FASTA + GTF)	`--whitelist` (10x barcode list), `--chemistry`
`simpleaf`	simpleaf index directory	`--chemistry`
`kb_python`	kallisto index file (`.idx`)	`--t2g` (transcript-to-gene map), `--chemistry`

sc-count

Source facts

Install options

Review the source files

More from this repository

More from this repository

🧬 Single-Cell Counting

Why This Exists

Core Capabilities

Input Formats

🧬 Single-Cell Counting

Why This Exists

Core Capabilities

Input Formats

Data / State Requirements

Beginner Setup Hint

Workflow

CLI Reference

Example Queries

Algorithm / Methodology

Cell Ranger Path

STARsolo Path

SimpleAF / Alevin-fry Path

kb-python Path

Visualization Contract

Output Structure

Reproducibility Contract

Knowledge Companions

Dependencies

Environment Management

CLI Parameters

R Enhanced Plots

Special Requirements

Reference Files

Direct Import (No Re-run)

Workflow Position