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rcannood committed Sep 8, 2024
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Expand Up @@ -41,7 +41,7 @@ Similarly, run the command for other methods.
## Evaluate a GRN

``` bash
scripts/run_evaluation.sh --grn resources/grn-benchmark/grn_models/collectri.csv
scripts/benchmark_grn.sh --grn resources/grn-benchmark/models/collectri.csv
```

Similarly, run the command for other GRN models.
Expand Down Expand Up @@ -100,11 +100,10 @@ approaches to assess both accuracy and comprehensiveness.

## Authors & contributors

| name | roles |
|:-------------------|:-------|
| Jalil Nourisa | author |
| Antoine Passemiers | author |
| Robrecht Cannoodt | author |
| name | roles |
|:------------------|:-------|
| Jalil Nourisa | author |
| Robrecht Cannoodt | author |

## API

Expand All @@ -115,26 +114,26 @@ flowchart LR
comp_metric[/"Label"/]
file_prediction("GRN")
file_score("Score")
file_prior("prior data")
file_multiomics_rna_h5ad("multiomics rna")
comp_method[/"Method"/]
file_multiomics_atac_h5ad("multiomics atac")
comp_method_r[/"Method r"/]
file_perturbation_h5ad---comp_control_method
file_perturbation_h5ad---comp_metric
comp_control_method-->file_prediction
comp_metric-->file_score
file_prediction---comp_metric
file_prior---comp_control_method
file_multiomics_rna_h5ad---comp_method
comp_method-->file_prediction
file_multiomics_atac_h5ad---comp_method
comp_method_r-->file_prediction
```

## File format: perturbation

Perturbation dataset for benchmarking.

Example file: `resources/grn-benchmark/perturbation_data.h5ad`
Example file: `resources_test/grn-benchmark/perturbation_data.h5ad`

Format:

Expand All @@ -160,15 +159,15 @@ Slot description:
| `obs["well"]` | `string` | Well name on the plate. |
| `obs["cell_count"]` | `string` | Number of single cells pseudobulked. |
| `layers["n_counts"]` | `double` | Pseudobulked values using mean approach. |
| `layers["pearson"]` | `double` | Normalized values using pearson residuals. |
| `layers["lognorm"]` | `double` | Normalized values using shifted logarithm . |
| `layers["pearson"]` | `double` | (*Optional*) Normalized values using pearson residuals. |
| `layers["lognorm"]` | `double` | (*Optional*) Normalized values using shifted logarithm . |

</div>

## Component type: Control Method

Path:
[`src/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/control_methods)
[`src/control_methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/control_methods)

A control method.

Expand All @@ -179,16 +178,16 @@ Arguments:
| Name | Type | Description |
|:---|:---|:---|
| `--perturbation_data` | `file` | Perturbation dataset for benchmarking. |
| `--layer` | `string` | Which layer of pertubation data to use to find tf-gene relationships. Default: `lognorm`. |
| `--prior_data` | `file` | Prior data used for grn benchmark. |
| `--layer` | `string` | (*Optional*) Which layer of pertubation data to use to find tf-gene relationships. Default: `scgen_pearson`. |
| `--prediction` | `file` | (*Output*) GRN prediction. |
| `--tf_all` | `file` | (*Optional*) NA. |

</div>

## Component type: Label

Path:
[`src/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/metrics)
[`src/metrics`](https://github.com/openproblems-bio/openproblems/tree/main/src/metrics)

A metric to evaluate the performance of the inferred GRN

Expand All @@ -198,19 +197,23 @@ Arguments:

| Name | Type | Description |
|:---|:---|:---|
| `--perturbation_data` | `file` | Perturbation dataset for benchmarking. |
| `--perturbation_data` | `file` | (*Optional*) Perturbation dataset for benchmarking. |
| `--prediction` | `file` | GRN prediction. |
| `--score` | `file` | (*Output*) File indicating the score of a metric. |
| `--score` | `file` | (*Optional, Output*) File indicating the score of a metric. |
| `--reg_type` | `string` | (*Optional*) name of regretion to use. Default: `ridge`. |
| `--subsample` | `integer` | (*Optional*) number of samples randomly drawn from perturbation data. Default: `-1`. |
| `--subsample` | `integer` | (*Optional*) number of samples randomly drawn from perturbation data. Default: `-2`. |
| `--max_workers` | `integer` | (*Optional*) NA. Default: `4`. |
| `--method_id` | `string` | (*Optional*) NA. |
| `--tf_all` | `file` | (*Optional*) NA. |
| `--apply_tf` | `boolean` | (*Optional*) NA. Default: `TRUE`. |

</div>

## File format: GRN

GRN prediction

Example file: `resources/grn-benchmark/collectri.csv`
Example file: `resources_test/grn_models/collectri.csv`

Format:

Expand All @@ -237,40 +240,14 @@ Slot description:

File indicating the score of a metric.

Example file: `resources/grn-benchmark/score.csv`

Format:

<div class="small">

Tabular data
'accuracy', 'completeness'

</div>

Slot description:

<div class="small">

| Column | Type | Description |
|:---------------|:---------|:-------------------------------|
| `accuracy` | `string` | (*Optional*) some explanation. |
| `completeness` | `double` | (*Optional*) some explanation. |

</div>

## File format: prior data

Prior data used for grn benchmark

Example file: `resources/grn-benchmark/prior_data.h5ad`
Example file: `resources_test/scores/score.h5ad`

Format:

<div class="small">

AnnData object
uns: 'tf_list'
uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values'

</div>

Expand All @@ -280,15 +257,18 @@ Slot description:

| Slot | Type | Description |
|:---|:---|:---|
| `uns["tf_list"]` | `list` | List of known tfs obtained from https://resources.aertslab.org/cistarget. |
| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. |
| `uns["method_id"]` | `string` | A unique identifier for the method. |
| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. |
| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |

</div>

## File format: multiomics rna

RNA expression for multiomics data.

Example file: `resources/grn-benchmark/multiomics_rna.h5ad`
Example file: `resources_test/grn-benchmark/multiomics_rna.h5ad`

Format:

Expand All @@ -313,27 +293,31 @@ Slot description:
## Component type: Method

Path:
[`src/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/methods)
[`src/methods`](https://github.com/openproblems-bio/openproblems/tree/main/src/methods)

A GRN inference method

Arguments:

<div class="small">

| Name | Type | Description |
|:--------------------|:-------|:--------------------------------------------|
| `--multiomics_rna` | `file` | RNA expression for multiomics data. |
| Name | Type | Description |
|:---|:---|:---|
| `--multiomics_rna` | `file` | (*Optional*) RNA expression for multiomics data. |
| `--multiomics_atac` | `file` | (*Optional*) Peak data for multiomics data. |
| `--prediction` | `file` | (*Output*) GRN prediction. |
| `--prediction` | `file` | (*Optional, Output*) GRN prediction. |
| `--temp_dir` | `string` | (*Optional*) NA. Default: `output/temdir`. |
| `--num_workers` | `integer` | (*Optional*) NA. Default: `4`. |
| `--tf_all` | `file` | (*Optional*) NA. |
| `--max_n_links` | `integer` | (*Optional*) NA. Default: `50000`. |

</div>

## File format: multiomics atac

Peak data for multiomics data.

Example file: `resources/grn-benchmark/multiomics_atac.h5ad`
Example file: `resources_test/grn-benchmark/multiomics_atac.h5ad`

Format:

Expand All @@ -355,3 +339,24 @@ Slot description:

</div>

## Component type: Method r

Path:
[`src/methods_r`](https://github.com/openproblems-bio/openproblems/tree/main/src/methods_r)

A GRN inference method

Arguments:

<div class="small">

| Name | Type | Description |
|:----------------------|:----------|:-------------------------------------------|
| `--multiomics_rna_r` | `file` | (*Optional*) NA. |
| `--multiomics_atac_r` | `file` | (*Optional*) NA. |
| `--prediction` | `file` | (*Optional, Output*) GRN prediction. |
| `--temp_dir` | `string` | (*Optional*) NA. Default: `output/temdir`. |
| `--num_workers` | `integer` | (*Optional*) NA. Default: `4`. |

</div>

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