Description

Perform differential splicing analysis using SUPPA.

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

1 ()

2 ()

3 ()

0 ()

1 ()

2 ()

3 ()

method (string)

Method to use for differential splicing analysis. Options are "empirical" or "classical".

local_area (integer)

Number of points in the local area of the delta PSI - average TPM distribution.

lower_bound_delta_psi (float)

Lower bound for the absolute delta PSI to test for significant. Events with less than this delta PSI will not be tested. Only valid for the "empirical" method.

is_paired (boolean)

Indicates if replicates across conditions are paired.

gene_correction (boolean)

Correction of the p-values by gene.

multi_testing_correction_alpha (float)

Family-wise error rate to use for the multiple testing correction.

save_tpm_events (boolean)

The average log TPM of the events will be saved in an external file.

combination_analysis (boolean)

SUPPA will perform the analysis between all possible combinations of conditions.

use_median_delta_psi (boolean)

SUPPA will use the median delta PSI, instead of the mean.

tpm_threshold (float)

Minimum expression (calculated as average TPM value within-replicates and between-conditions) to be included in the analysis.

nan_tpm_threshold (float)

Proportion of samples with nan values allowed per condition to calculate a delta PSI.

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

Tools

suppa Documentation

Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.

doi: 10.1186/s13059-018-1417-1License: MIT
Authors