WheatFlagLeafSenescence

Scripts for the manuscript 'Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling'

1) Mapping

Map samples with kallisto

2) Merge samples

Merge tpm and counts into a single table for all samples

3) Differential expression

a) With gradient tool

Prepare data for gradient tool on cyverse

Arrange output data from gradient tool into patterns for zscore > |2|

b) With ImpulseDE2.

ImpulseDE2 This also merges together the gradient tool and ImpulseDE2 results

4) GO enrichment of patterns

GO term enrichment of grouped patterns with goseq

5) Prepare data for CSI

Prepare data for CSI