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NF_LandscapePaper_2019

This repository hosts all the code used to generate analyses and figures for the landscape paper.

Notebooks

Here is a summary of the notebooks contained in the Results folder:

File Description
01-MultiPLIER-Expression-by-Sex We evaluate the latent variable expression in NF tumors as it pertains to the sex of the patient the sample was derived from.
02-TumorDeconvBySex A first stab at checking immune annotation predictions to see if the presence/absence of immune cells is any different between sexes.
03-DeconvMetaviperCor A comparison of tumor immune scores to metaviper predictions in NF tumors.
04-GSVA-sex-differences Sex differences in GSVA pathway enrichment in NF tumors.
05-TumorDeconvHeatmaps Code for heatmapping the immune deconvolution results of all NF tumors.
06-CutNFPatVars Plotting/correlating gene expression to cutaneous neurofibroma tumor/patient metadata.
07-ImmuneDeconv-LatentVariableCorrelation Correlation of multiPLIER latent variable expression to immune deconvolution results.
08-CNFGrowth-ImmuneCor Correlating immune deconvolution results to cutaneous NF tumor/patient metadata (i.e. size, itching).
09-CNFMetadata-LVCor Correlation cNF metadata such as itching and tumor size with latent variables
10-pNF-ProgressionImmune Evaluating differences in immune populations between patients that get MPNSTs vs those that do not
11-immuneByGeneVariant Testing gene mutations for significant alterations in immune populations
12-Interesting-LVs-in-recount2 We looked for interesting latent variables, and tried to samples in the recount2 data that were correlated to the NF LV expression. We also looked for interesting LVs that are different between pNF and MPNST.
13-kruskal-wallis-lvs-pan-nf.html We looked for significant latent variables as a function of tumor type by performing kruskall-wallis tests.
14-kruskal-wallis-immune-pan-nf.html We looked for significantly different immune cell signatures as a function of tumor type by performing kruskall-wallis tests.
15-RandomForest-LVs.html We looked at the highly variable LVs in NF1 and used them to model a classifier to find features (LVs) that identify various tumorTypes.
16-LatentVar-metaviperCor.html Here we sought to identify metaviper protein activity with specific latent variables to provide specific biological relevance.
17-LV-GenomicVariantTest.html Here we searched for genes that, when mutated, cause a difference in LV values.
18-lv-drug-target-enrichment.html This analysis focuses on identifying which LVs are enriched in all druggable genes.

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This repository hosts all the code used to generate analyses and figures for the landscape paper

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