To do (bioinformatics)

[plger]

Bioinformatics

RNAseq:

Between each combination of successive timepoints:

• [ ] pathway enrichment analysis across timepoints
• [ ] vGSEA and ssGSEA
• [ ] miRNA target enrichment analysis
  • [ ] mirnet
  • [ ] enrichMir
• [ ] transcription factor target enrichment analysis
  • [ ] method from the montreal dude
  • [ ] define target genes using the ATACseq, then do GSEA or something similar on those sets
• [ ] cluster genes on the basis of their pattern across all timepoints

Short RNA seq

• [ ] ncPRO analysis
• [ ] shortRNA analysis
• [ ] describe the types of RNAs observed
• [ ] does one observe changes in miRNAs whose targets when enriched among the RNAseq alterations?
• [ ] can one explain changes in short RNAs from transcription factor bindings?

RRBS

• [ ] overview of the methylation pattern
  • [ ] pathway/over-representation analysis (GREAT)
• [ ] comparison with ES and sperm (rando) :
  • [ ] what are the regions/loci that, in SCs, are like ES, or like sperm?
  • [ ] what are the regions that get methylated/unmethylated from one step to the next?
  • [ ] are these regions enriched from TF motifs?

ATACseq

• [ ] identify accessible TF binding sites at each timepoint
• [ ] run differential accessibility and differential TF activity
• [ ] compare with predictions from RNAseq

Integration

• [ ] mixOmics
• [ ] MOFA
• [ ] integrated miRNA and TF targets into a network