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Rob Reid's Projects

blueberryandgage icon blueberryandgage

Pathway level analysis is often done at a gene level perspective. Here, we utilize the GAGE pathway analysis tool to explore the most active pathways in blueberry at different stages of berry development. Here are scripts involved in Gage / Pathview in R. As well as command line scripts for various stages. The code is designed to run on our local cluster and will need heavy tweaking to be of utility elsewhere.

dp_gp_cluster icon dp_gp_cluster

Clustering gene expression time series data using an infinite Gaussian process mixture model. Goal to implement this on time series RNA-Seq data.

sweetpotatorna-seq icon sweetpotatorna-seq

A small collection of scripts for various stages of Sweet potato RNA-Seq analysis

tomato-rnaseq-scripts icon tomato-rnaseq-scripts

This is a collection of scripts for analyzing featurecount data by way of deseq2, EdgeR, EBEQ-HMM.

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