baredsc/baredSC-1d-logNorm
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Tests Applies baredSC algorithm to fit and combine one-dimensional Gaussian mixture models (from 1 to N components) on log-normalized single-cell gene expression data. Enables identification of subpopulations based on expression of genes of interest and provides statistical assessment of the optimal number of components in heterogeneous cell populations.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Gene name | Gene name | Must be included in the first row of the tabular |
|
| Maximum number of Gaussians to study | Maximum number of Gaussians to study | Usually 4 is enough |
|
| Maximum value in logNorm | Maximum value in logNorm | Maximum value to explore in logNorm |
|
| Tabular with raw expression values | Tabular with raw expression values | The dataset must have a first row with row names. Among them should be 'nCount_RNA' and the gene you want to get PDF of. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | generate_param_list_one_to_number | n/a |
| 5 | baredSC | toolshed.g2.bx.psu.edu/repos/iuc/baredsc_1d/baredsc_1d/1.1.3+galaxy0 |
| 6 | combine baredSC 1d | toolshed.g2.bx.psu.edu/repos/iuc/baredsc_combine_1d/baredsc_combine_1d/1.1.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| baredsc_qc_plots | baredsc_qc_plots | n/a |
|
| baredsc_neff | baredsc_neff | n/a |
|
| baredsc_numpy | baredsc_numpy | n/a |
|
| combined_pdf | combined_pdf | n/a |
|
| combined_plot | combined_plot | n/a |
|
| combined_other_outputs | combined_other_outputs | n/a |
|
Version History
v0.1 (earliest) Created 21st Oct 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
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v0.151a4752
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Views: 5555 Downloads: 1044 Runs: 0
Created: 21st Oct 2023 at 03:01
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