Pinned Repositories
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.
Cluster-Scripts
From HPC
DOI_request_quickstart
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.
EchinoSpecies
Elegoo-Neptune-4-Series
all my work on the neptune 4 series
Machine-Learning-AndrewNg-DeepLearning.AI
Contains all course modules, exercises and notes of ML Specialization by Andrew Ng, Stanford Un. and DeepLearning.ai in Coursera
pathview
SweetPotatoRNA-Seq
A small collection of scripts for various stages of Sweet potato RNA-Seq analysis
Tomato-RNASeq-scripts
This is a collection of scripts for analyzing featurecount data by way of deseq2, EdgeR, EBEQ-HMM.
bioinformagical's Repositories
bioinformagical/Cluster-Scripts
From HPC
bioinformagical/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.
bioinformagical/DOI_request_quickstart
bioinformagical/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.
bioinformagical/EchinoSpecies
bioinformagical/Elegoo-Neptune-4-Series
all my work on the neptune 4 series
bioinformagical/Machine-Learning-AndrewNg-DeepLearning.AI
Contains all course modules, exercises and notes of ML Specialization by Andrew Ng, Stanford Un. and DeepLearning.ai in Coursera
bioinformagical/medium
bioinformagical/pathview
bioinformagical/reproducibility-tutorial
Cyverse tutorial of assembling FP
bioinformagical/scripts-cluster
All of the cluster scripts since 2011
bioinformagical/SweetPotatoRNA-Seq
A small collection of scripts for various stages of Sweet potato RNA-Seq analysis
bioinformagical/Tomato-RNASeq-scripts
This is a collection of scripts for analyzing featurecount data by way of deseq2, EdgeR, EBEQ-HMM.