mxhp75 / honoursthesis

All R Markdown scripts for the final thesis

honoursThesis

All R Markdown scripts for the final thesis

** All files currently on my VM **

Includes

testAlign.sh

• 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

placentaDifferentialExpression.Rmd

• Placenta Differential Expression analysis between female and male-bearing pregnancy
  • filtering and normalisation in edgeR
  • lm in limma
  • volcano plots

placentaDifferentialExpressionHypoxic.Rmd

• Placenta Differential Expression analysis between low and normoxic oxygen environment
  • filtering and normalisation in edgeR
  • lm in limma
  • volcano plots

placentaProfile.Rmd

• Global Placenta Expression Profile
  • filtering and normalisation in edgeR
  • Heat maps of expression (lcpm)

plasmaDifferentialExpression.Rmd

• Maternal Plasma Differential Expression analysis between female and male-bearing pregnancy
  • filtering and normalisation in edgeR
  • lm in limma
  • volcano plots

plasmaDifferentialExpression.Rmd

• Maternal Plasma Differential Expression analysis between low and normoxic oxygen environment
  • filtering and normalisation in edgeR
  • lm in limma
  • volcano plots

plasmaProfile.Rmd

• Global Placenta Expression Profile
  • filtering and normalisation in edgeR
  • Heat maps of expression (lcpm)

C19MC.Rmd

• 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)

miR_371_3.Rmd

• 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)

C14MC.Rmd

• 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)

allClusterProfile.Rmd

• 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

honoursthesis's Issues

Initital supervisor edits and comments

Looks good but you probably want to separate that first code chunk into 3 or 4.

i.e.

1. Import the data files
2. filtering/editing metadata
3. Subsetting a categorising
4. Summary tables