NK Cell Response to Influenza A Viruses

This is the code repository to reproduce all major figures in our paper:

L. Kronstad, C. Seiler, R. Vergara, S. Holmes, and C. Blish
Differential Induction of IFN-α and Modulation of CD112 and CD54 Expression Govern the Magnitude of NK Cell IFN-γ Response to Influenza A Viruses
The Journal of Immunology, 2018

Installation

make install

Using STAR.

make mapping

Using tophat.

make indexing
make mapping_tophat

This will run two R markdown files: DESeq2.Rmd and NetworkAnalysis.Rmd.

make da_monocyte
make da_nk

Name		Name	Last commit message	Last commit date
Latest commit History 190 Commits
.DS_Store		.DS_Store
.gitignore		.gitignore
Alignment_STAR.bash		Alignment_STAR.bash
Alignment_STAR.sbatch		Alignment_STAR.sbatch
Alignment_STAR_Virus.bash		Alignment_STAR_Virus.bash
Alignment_STAR_Virus.sbatch		Alignment_STAR_Virus.sbatch
Alignment_tophat.bash		Alignment_tophat.bash
Alignment_tophat.sbatch		Alignment_tophat.sbatch
DESeq2.Rmd		DESeq2.Rmd
DESeq2_monocyte.sbatch		DESeq2_monocyte.sbatch
DESeq2_nk.sbatch		DESeq2_nk.sbatch
ImmunologyLisa.Rproj		ImmunologyLisa.Rproj
Indexing_STAR.sbatch		Indexing_STAR.sbatch
Installation.bash		Installation.bash
Installation_R_only.bash		Installation_R_only.bash
Makefile		Makefile
NetworkAnalysis.Rmd		NetworkAnalysis.Rmd
README.md		README.md
README_legacy.md		README_legacy.md
RNA-Seq M and NK File Names.xlsx		RNA-Seq M and NK File Names.xlsx
Virus.Rmd		Virus.Rmd
Virus.sbatch		Virus.sbatch
export_geo_upload.R		export_geo_upload.R
lookup_sequence.Rmd		lookup_sequence.Rmd
sample_table_monocyte_H1N1_UI.csv		sample_table_monocyte_H1N1_UI.csv
sample_table_monocyte_all.csv		sample_table_monocyte_all.csv
sample_table_nk_H1N1_UI.csv		sample_table_nk_H1N1_UI.csv
sample_table_nk_all.csv		sample_table_nk_all.csv