Mechanobiology, Wolfson et al. 2024

Code for all bulk RNA-sequencing analyses in Wolfson et al. 2024.

Bulk RNA-sequencing differential expression

Differential expression analysis with DESeq2:

• DESeq2/Mechanobiology_DESeq2_V1.Rmd

NicheNet analysis

Examining potential downstream receptors and targets of DE ligands:

• NicheNet/LR_NicheNet_Setup_V1.Rmd: Grouping cell types in the Drokhlyansky et al. 2020 human data
• NicheNet/LR_NicheNet_Setup_V2.Rmd: Re-labeling smooth muscle cell types in the Drokhlyansky et al. 2020 human data
• NicheNet/LR_NicheNet_Analysis_loadedUP_V4.Rmd: NicheNet anaysis for ligands UP in the loaded condition
• NicheNet/LR_NicheNet_Analysis_unloadedUP_V4.Rmd: NicheNet anaysis for ligands UP in the unloaded condition