Tools for quantitative analyses of diatom resilience.

library.py: library containing the common functions, including the fitting functions.
timeSeriesFitter.py: script to fit each time series individually with the purpose of manually checking the goodness of fit.
epochGrapher.py: script to generate the epoch figures for each condition.
nicheBreadthGrapher.py: script to generate the niche breadth increase based on maximum growth.
tippingPointTransitionGrapher.py: script to generate the tipping point transition based on growth lag and carrying capacity.

The natural order for the analysis would follow as:

readsCleaner.py: script to call Trimmomatic and clean the reads.

readsMapper.py: script to call STAR and map the reads to the genome.

readsCounter.py: script to call HTSeq to counts the reads per transcript.

cufflinksCaller.py: script to call cufflinks and quantify the mapped reads.

classifiersFinder.py: script that calls cuffdiff to find DETs between two conditions.
carbonFixationAnalyser.py: script that calls cuffdiff to find DETs between LC and HC for specific CCM transcripts.

samplesCorrelationGrapher.py: script to compute and plot the correlation among samples. Available both on counts and FPKM values.
pcaGrapher.py: script to compute the PCA on expression values in FPKM.
sampleMapper.py: script to map samples into diurnal and growth coordinates.
GSE_Mapper.py: script to map samples into diurnal and growth space from microarray data.

logValuesMatrixCreator.py: script to transform absolute (FPKM) into relative expression (log2 fold change). cartoonFigureGenerator.py: script to generate a cartoon about the state space calculation.