** All files currently on my VM **
Includes
- Bash script for the test alignment using secondary pipeline
- Adapter trimming = cutadapt
- Seqence alignment = STAR
- Known small RNA quantification = SeqCluster
- Novel miRNA prediction = miRDeep2
- Other small RNA quantification = SeqBuster
- Placenta Differential Expression analysis between female and male-bearing pregnancy
- filtering and normalisation in edgeR
- lm in limma
- volcano plots
- Placenta Differential Expression analysis between low and normoxic oxygen environment
- filtering and normalisation in edgeR
- lm in limma
- volcano plots
- Global Placenta Expression Profile
- filtering and normalisation in edgeR
- Heat maps of expression (lcpm)
- Maternal Plasma Differential Expression analysis between female and male-bearing pregnancy
- filtering and normalisation in edgeR
- lm in limma
- volcano plots
- Maternal Plasma Differential Expression analysis between low and normoxic oxygen environment
- filtering and normalisation in edgeR
- lm in limma
- volcano plots
- Global Placenta Expression Profile
- filtering and normalisation in edgeR
- Heat maps of expression (lcpm)
- Sub set of placenta and plasma expression profiles with only miRNA from the chromosome 19 mega cluster
- filtering and normalisation in edgeR
- Heat maps of expression (lcpm)
- Sub set of placenta and plasma expression profiles with only miRNA from the chromosome 19 cluster miR-371-3
- filtering and normalisation in edgeR
- Heat maps of expression (lcpm)
- Sub set of placenta and plasma expression profiles with only miRNA from the chromosome 14 mega cluster
- filtering and normalisation in edgeR
- Heat maps of expression (lcpm)
- Sub set of placenta and plasma expression profiles with chromosome 14 and 19 clusters combined
- filtering and normalisation in edgeR
- Heat maps of expression (lcpm)
- correlation