niehaus2021's Introduction

Mouse spinal cord during neuropathic pain.

This is a repository for code used in the publication Niehaus et al. 2021 entitled "Spinal cord macrophages resolve nociceptive hypersensitivity after peripheral injury".

Example script files for several components of the paper

Code for the Shiny online application (zylka-lab.med.unc.edu):

app.R - This code should be straightforward, with instructions I used to generate this application available at 'https://rstudio.github.io/shiny/tutorial/'.
avgbar_lattice.R and propbar_lattice.R - Plotting functions

A general pipeline for single-cell RNA-seq (scRNAseq) dataprocessing and the source file used to generate plots; adapted from Loo et al. 2019 and Shekhar et al.2018.

scRNAseq - Directory with scripts used for two rounds of clustering from initial genes x cells dataframe (available at GEO GSE134003). This pipeline was adapted from the above publications, whose pipelines are found at 'https://github.com/jeremymsimon/MouseCortex' and 'https://github.com/broadinstitute/BipolarCell2016'. Clustering began with with an initial round followed by subclustering of each initial cluster.

Example scripts of immunofluorescence analyses via imageJ (Fiji).

autoAdjust.ijm - autoAdjust macro for Fiji; must be installed for GFAP and IBA1 quantification
GFAParea.ijm Quantifies GFAP area per ROI area from maximum intensity projection image (GFAP = channel 1)
IBA1area_and_cells.ijm Quantifies IBA1 area and number of IBA1 DAPI cells from maximum intensity projection image (DAPI = channel 1, IBA1 = channel 2)

Example Rscript for testing and visualization used in the manuscript