Suppa

- New Differential transcript usage option
- Modified generateEvents option for generating ioe or ioi files (-f)

New options for diffSplice:
-- combination: SUPPA perform the differential splicing calculation between all the possible combinations of conditions
-- median: SUPPA use the median to calculate Delta PSI instead of the mean
--tpm-threshold: minimum transcript average TPM value within-replicates and between-conditions to be included in the analysis
--save_tpm_events: the average log TPM of the events will be saved in an external file
--tpm-threshold: Minimum transcript average TPM value within-replicates and between-conditions to be included in the analysis

Incoporated pip installation

SUPPA isoform compatible extension. Modifications:

1. generateEvents: has a new required argument (-f --format) which can be either ioe or ioi. If the choosen format is ioe the programs requires the at least one event type is assigned to -e (for ex: SE). The rest of the commands for this functionality works as in the previous version.
2. diffSplice:
- The argument --expression-files was changed to --tpm (it is more intuitive and faster to type).
- The argument --ioe was changed to --input. This argument checks if the file has either an .ioe or .ioi file extension. If not. the programs exist with an error informing the user about this. The rest of the commands for this functionality works as in the previous version.

Stable v2.0 of SUPPA