Included files and description


run_analysis.py
	python script that executes the analysis pipeline.

GO_analysis/ChartReport.py
	Runs a chart report request on the David web service
GO_analysis/DAVIDWebService_Client.py
	Client script for David web service query
GO_analysis/DAVIDWEBREADME.txt
	Readme file for david web service scripts
GO_analysis/FuncClust.py
	Runs a functional cluster request on the David web service
GO_analysis/go_rise.py
	Calculates the average time it takes for all proteins in a GO term
	to begin changing (t1 in main txt).
GO_analysis/id_convert.p
	Converts Accession to Entrez ID
GO_analysis/mean_of_genes_in_go_term_mRNA.py
	Averages the gene expression profiles that are contained in a given GO term. 
GO_analysis/readcsv.py
	C simple script to read in txt delimeted files



data/Oi_name_map.p
	Pickle file, gives the apex OI values indexed by their common names.
data/Test_data.csv 
	Gives some test RNA raw count data. Unit test for RNA normalization and data formatting
data/Test_data_answers.xlsx
	Gives the test RNA raw count data answers to normalization and data formatting
data/Test_name_map.p
	Maps the accession to entrez IDs for querying DAVID webservice
data/emili_orphan_predictions_ecoli.csv
	Emili lab computational predictions of gene functions downloaded from publication <cite>.
data/prot_data.csv
	Raw protein counts
data/rna_data.csv
	Raw rna counts
data/rna_name_map.csv
	Maps the RNA (ECB number) to Entrez accession.


data_processing/cluster_kmeans.py
	Preform k-means clustering and plot the results
data_processing/format_data.py
	Processes count data as described in main text. normalizes counts using read depth.
data_processing/format_data_deseq.py
	Process count data. normalize counts using DEseq results
data_processing/format_data_norm_to_length.py
	Process count data.normalize counts by transcript length (for absolute comparison)
data_processing/format_data_wapex.py
	Process count data. Normalize counts using APEX OI values (for absolute comparison)
run_analysis.py


Figures/
	Contains figures of publication

fit_time_course/time_course_fit.py
	Script that fit's piecewise continuous curve to expression profiles. Uses custom implimination of Differential Evolution algorthim.
fit_time_course/classify_fits.py
	Sort fits based upon parameters estimated from fitting the piecewise continous curve.


operon_analysis/operon_analysis_and_cluster_prot.ipynb
	ipython notebook script for creating correlation of expression profiles within operons

operon_analysis/OpersonSet2.txt
	List of operons downloaded from RegulonDB.