test to see if works on linux

FiguresForManuscript

This repo will contain all scripts used to produce the figures found in the manuscript

Figure 1

PCA plot:

Step1: figure1_importSalmonTranscriptResults.R

Step2: figure1_exploratory_visualization_PCA_heatmap.R

boxplot lincRNA genes V. PCG:

Step1:figure1_boxplot_comparisonPCG_lncRNA.R

Violin plot lincRNA gene expression:

Step1:figure1_violinplot_GloballincRNAexpression.R

Point plot sum "daily" expression:

Step1:figure1_PointPlotSum_lincRNA.R

Volcano plot lincRNA day0 v. day60:

Step1:figure1_VolcanoPlot_lincRNAlabeled.R

Heatmap lincRNA expression:

Step1:figure1_importSalmonTranscriptResults.R

Step2:figure1_LRT_timeseries_deseq2.R

Step3:figure1_normalizedCounts_heatmap.R

Figure 2

Heatmap of all DE lincRNA

Step 1: figure2_SpearmanCorr_DElincRNA.R

Network of DE lincRNA with correlation score of 0.9 with one another

Step 1: figure2_networkFor_DElincRNA.R

Topological Attributes for the DE lincRNA Network

Step 1: Functions_TopolgicalFeatures.R -- list of functions needed for Step #2

Step 2: figure2_NetworkTopologicalCharacteristics_lincRNA_lincRNA.R

XLmhg Analysis

Step 1: figure2_XLmhg_TopAttributes.R

Step 2: XLmhg.py --> Python script since the package is a Python package

Individual Hubs

Step 1: figure2_IndividualNetwokrsForHubs_lincRNA_lincRNA.R

Figure 3

Heatmap of all DE lincRNA transcripts

Step 1: figure3_transcriptAnalysis_DTU.R Step 2: figure3_DElincRNAisoformExpression.R

GOchord plot of lincRNA transcripts

Step 1: figure3_GoPlot_DEtranscripts.R

Table Summary of lincRNA transcript switches

Anecdotic examples of lincRNA switches

Figure 4

Fuzzy Clustering of DE lincRNAs and TFs

Barplots of TFs and lincRNA in each cluster

Number of lincRNAs highly correlated with the TF markers

Network of TF markers with highly correlated lincRNAs

Results of a hypergeometric test for each TF marker with ChIP data

Anecdotic examples of TF markers bidning to lincRNAs found in high correlation