danoreper

danoreper.github.io

exit

Code to support seq pipeline for "The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection" (Perkowski et. al. 2016)

IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

ISVdb

Code to support 'Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders' (Daniel Oreper, Yanwei Cai, 2017)

mnp2018

Code to generate results for 'Reciprocal F1 hybrids of two inbred mouse strains reveal parent-of-origin and perinatal diet effects on behavior and expression' (Oreper, Schoenrock, 2018)

ovx.demo

Demo code drawn from my analysis of ovariectomy data (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289389/), focusing on a single analysis. Intended to demonstrate Bayesian modeling of strain-by-treatment effects, and R usage, with ample comments.

ovx2016

Code for analyses in "Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice." ( Schoenrock, Oreper, 2016)

wdl

Workflow Description Language - Specification and Implementations

exit

Code used in the EXIT paper for sequence processing/analysis.

danoreper/ISVdb

Code to support 'Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders' (Daniel Oreper, Yanwei Cai, 2017)

danoreper/mnp2018

Code to generate results for 'Reciprocal F1 hybrids of two inbred mouse strains reveal parent-of-origin and perinatal diet effects on behavior and expression' (Oreper, Schoenrock, 2018)

danoreper/danoreper.github.io

danoreper/exit

Code to support seq pipeline for "The EXIT Strategy: an Approach for Identifying Bacterial Proteins Exported during Host Infection" (Perkowski et. al. 2016)

danoreper/IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

danoreper/ovx.demo

Demo code drawn from my analysis of ovariectomy data (see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289389/), focusing on a single analysis. Intended to demonstrate Bayesian modeling of strain-by-treatment effects, and R usage, with ample comments.

danoreper/ovx2016

Code for analyses in "Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice." ( Schoenrock, Oreper, 2016)

danoreper/wdl

Workflow Description Language - Specification and Implementations