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Thomas Wodarek 571465570b Changed it back to normal workflow.
2014-11-17 01:54:57 -08:00
results/cleanTSSerResults Added other results files 2014-09-29 00:03:18 -04:00
.hgignore Added .hgignore. Hopefully this works. 2014-06-10 18:43:51 -04:00
add_nearest_gene.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
add_nearest_gene.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
bedweight_analysis.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
bedweight_analysis.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
check_python_libraries.py Added MPI4Py at the top level to allow for parallel actions mid-stream. Also accounted for in the start-up script. 2014-08-18 02:41:22 -07:00
convert_protein_table.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
convert_protein_table.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
convert_rna_table.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
convert_rna_table.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
expression_enrichment_2.py All data clean through the end of step 11. More hackery, but worth it. 2014-10-26 00:18:29 -07:00
expression_enrichment_2.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
find_nearestGeneN.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
find_nearestGeneN.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
find_nearestGeneP.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
find_nearestGeneP.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
generate_oriented_extended_clusters Added generate_oriented_extended_clusters binary and the generate sample names script. 2014-10-19 21:05:38 -07:00
hosts Fixed np value and hosts file. 2014-11-16 23:52:16 -08:00
merge_paramest.py Cleaning up syntax errors and hunting those pesky logic errors. 2014-11-17 00:24:59 -08:00
non_rna_TSS_info.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
non_rna_TSS_info.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
paramEst_zscore.py Cleaning up stuffs and figuring out why step13 summary generation doesn't exactly work. Untagged summaries to clean up. 2014-11-16 23:50:22 -08:00
README README edited online with Bitbucket 2014-10-27 08:53:08 +00:00
remove_structural_RNA.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
remove_structural_RNA.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
runMainZScore.py Changed it back to normal workflow. 2014-11-17 01:54:57 -08:00
runZScore.sh Cleaning up syntax errors and hunting those pesky logic errors. 2014-11-17 00:24:59 -08:00
sample_names_generator.sh Added generate_oriented_extended_clusters binary and the generate sample names script. 2014-10-19 21:05:38 -07:00
step13DebugSkip.py Adding initial part of the Step 13 bypass. 2014-11-17 01:54:03 -08:00
step15.py The first pass of the code is done with step 15 pretty printing out the final results. 2014-11-17 00:38:39 -08:00
stepXII.py Working on getting Step 13 clear of problems (with parallelism). 2014-10-26 04:52:04 -07:00
temp Complete through end of Step 8. Still some bugs though... 2014-06-11 10:48:59 -04:00
tempNotes Step XIII nearly complete (still needs bug stomping though). 2014-07-30 02:39:58 -04:00
TSS_info_across_samples.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
TSS_info_across_samples.pyc Complete through end of Step 8. Still some bugs though... 2014-06-11 10:48:59 -04:00
TSS_info_across_samples_zscore.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
TSS_info_across_samples_zscore.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
TSSer_log Sync to import into Eclipe 2014-10-19 22:21:57 -07:00
TSSselection_local_zscore_version_category_norm.py Cleaning up syntax errors and hunting those pesky logic errors. 2014-11-17 00:24:59 -08:00
TSSselection_local_zscore_version_category_norm_paramEst.sh 5pm checkpoint 2014-06-11 17:02:10 -04:00
zscore_across_samples.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
zscore_across_samples.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00
zscore_calc.py Changing my email from thomas.wodarek<at>gmail.com to twodarek<at>acm.org 2014-10-26 00:22:47 -07:00
zscore_calc.pyc Data is clean through the end of step 12. 2014-10-26 03:26:23 -07:00

README 

Original version by: Jorjani H., Zavolan M. Computational and Stsyems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
  Paper: TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.
Modified version by: Thomas Wodarek <twodarek<at>acm.org> of the Computer Science Department of Calvin College, United States of America.

This is a reworking of TSSer to clean up inefficiencies (like making this thing I/O bound!) and allowing for parallelization.

The original TSSer can be found at http://www.clipz.unibas.ch/downloads/TSSer/index.php and the sample dataset at http://www.clipz.unibas.ch/downloads/TSSer/input_example.zip.