GitLab

An R program to visualize, normalize, and analyze -omics data such as those from microarray, metabolomics and proteomics experiments. Data are supplied as a list or table along with parameter settings, all in an Excel file.

An example workflow package for the BioHPC Astrocyte workflow engine.

basic useful copy-and-paste type codes

Source codes to perform simulations of microtubule growth. Cleary et al. 2022, Elife, "Measurements and simulations of microtubule growth imply strong longitudinal interactions and reveal a role for GDP on the elongating end".

TAD aware Regulatory Network Construction (TReNCo). The package provides scripts for constructing cell-type specific mouse TF-gene networks.

Testing for data normality and variability, reporting sample sizes, and visualizing data groups.

A single-cell RNA-seq analysis workflow for data stored on the BioHPC using CellRanger and Seurat.

Low-frequency small variants and large deletions detection from mitochondrial DNA deep sequencing experiments.