> ## Documentation Index
> Fetch the complete documentation index at: https://docs.bioptimus.com/llms.txt
> Use this file to discover all available pages before exploring further.

# bioptimus.data.omics.bulkrna

Bulk RNA-seq data reader.

Provides `BulkRNAData` — a lightweight wrapper around a CSV/TSV of gene expression counts for a single patient sample.

**Wide format** (default) — one row per sample, genes as columns:

```text theme={null}
sample_id,gene_1,gene_2,...,gene_N
patient_001,12.3,4.5,...,0.1
```

The first column is treated as the sample identifier (index). All remaining columns are gene expression values. Only the first row is used; additional rows are ignored.

**Long format** — one row per gene, activated by setting `gene_column` and `value_column`:

```text theme={null}
gene_name,raw_count,normalized
gene_1,12.3,0.5
gene_2,4.5,0.2
```

The separator is inferred from the file extension (`.tsv` → tab, otherwise comma) but can be overridden via `separator`.

## BulkRNAData

```python theme={null}
class BulkRNAData()
```

Single-sample bulk RNA-seq counts for PyTorch pipelines.

Reads a CSV or TSV with gene expression counts and stores the values as a contiguous `np.float32` array for zero-copy tensor creation via `counts`.

Supports two layouts:

* **Wide** (default): one row per sample, genes as columns. The first column is the sample identifier (index).
* **Long**: one row per gene, activated by setting `gene_column` and `value_column`.

<ParamField body="path">
  Path to the CSV or TSV file.
</ParamField>

<ParamField body="gene_names">
  Optional gene list to filter/align columns to. Missing genes are zero-filled, extras are dropped. When `None` all columns are kept.
</ParamField>

<ParamField body="omic_transform">
  Optional preprocessing transform applied when accessing `counts`.
</ParamField>

<ParamField body="separator">
  Column delimiter. When `None` the separator is inferred from the file extension (`.tsv` → tab, otherwise comma).
</ParamField>

<ParamField body="gene_column">
  Column name that contains gene identifiers. Required for long-format files.
</ParamField>

<ParamField body="value_column">
  Column name that contains expression values to read. Required for long-format files.
</ParamField>

<ParamField body="sample_name">
  Sample identifier (first row index in wide format, or the file stem in long format).
</ParamField>

<ParamField body="gene_names">
  Ordered list of gene column names.
</ParamField>

#### num\_genes

```python theme={null}
@property
def num_genes() -> int
```

Number of gene columns.

#### counts

```python theme={null}
@property
def counts() -> list[float]
```

Gene counts as a list of floats.

#### get\_counts

```python theme={null}
def get_counts(sample_name: str | None = None) -> list[float]
```

Return gene counts as a flat sequence.

When no `omic_transform` is configured, returns a plain `list[float]`.  With a transform, returns the transform output (typically an `np.ndarray`).

<ParamField body="sample_name" type="str | None">
  Ignored (kept for backward compatibility).
</ParamField>

<ResponseField name="returns" type="list[float]">
  Gene expression values in column order.
</ResponseField>