marcottelab/AG3C_starvation_tc

Name: AG3C_starvation_tc

Owner: The Marcotte Lab

Description: null

Created: 2014-03-04 20:44:14.0

Updated: 2016-09-07 20:05:42.0

Pushed: 2016-09-07 20:05:41.0

Homepage: null

Size: 98829

Language: OpenEdge ABL

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README

AG3C

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.