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EvanForsythe
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ERCnet
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Line 156 in Phylogenomics.py has a typo
#97
tgattsIV
opened
1 year ago
0
Update README.md
#96
EvanForsythe
closed
1 year ago
0
Get Corr_meta_stats.R working again
#95
tgattsIV
opened
1 year ago
0
Update Readme to include sample data set instructions
#94
tgattsIV
opened
1 year ago
0
Adds Sample Dataset
#93
tgattsIV
closed
1 year ago
0
Change -r MinR param in Phylogenomics.py to have a default value derived from the number of species provided, rather than be hardcoded.
#92
tgattsIV
closed
1 year ago
0
Check all example commands in readme to make sure they're up to date
#91
EvanForsythe
opened
1 year ago
0
Investigate using uncapped memory for Joblib parallel workers
#90
tgattsIV
opened
1 year ago
0
Solving Issues
#89
tgattsIV
closed
1 year ago
0
removed bad line at end of R script
#88
EvanForsythe
closed
1 year ago
0
Tony bug fix branch
#87
tgattsIV
closed
1 year ago
0
Managing conflicts
#86
tgattsIV
closed
1 year ago
0
Func nets
#85
EvanForsythe
closed
1 year ago
0
Important: ERC 'hits' should be filtered so they don't include hits with negative slopes
#84
EvanForsythe
closed
1 year ago
1
updated Networks_and_stats.R to improve the centrality statistics csv
#83
EvanForsythe
closed
1 year ago
0
Include test dataset in repo
#82
EvanForsythe
closed
1 year ago
0
ERC_analyses.py error tracking to Branch_length_reconciliation.R
#81
EvanForsythe
closed
1 year ago
0
The -r argument in Phylogenomic.py has a default value of 10, which doesn't make sense for analyses with <10 species.
#80
EvanForsythe
closed
1 year ago
0
Network_stats_metrics csv file has duplicate rows
#79
EvanForsythe
closed
1 year ago
1
Network and Stats.R script has filename errors.
#78
tgattsIV
closed
1 year ago
0
Fix end of step argument recommendations and the README.txt
#77
tgattsIV
closed
1 year ago
0
Networks_and_analyses.py is broken due to file import issues, naming convention used, column headers.
#76
tgattsIV
closed
1 year ago
1
Fix underscore append at end of filename in ERC_Analyses.py
#75
tgattsIV
closed
1 year ago
1
Removes reference to corrMethod and the need for that line param
#74
tgattsIV
closed
1 year ago
0
Add filter to network communities that removes "peripheral" nodes
#73
EvanForsythe
opened
1 year ago
0
Refactor ERC_analyses.py to perform pearson and spearman in one run
#72
EvanForsythe
closed
1 year ago
1
Function decomposition and filename collision tony
#71
tgattsIV
closed
1 year ago
0
Fix bench test feature tony
#70
tgattsIV
closed
1 year ago
0
Hardcodes Phylogenomics parallel branches to be 1 except RaxML
#69
tgattsIV
closed
1 year ago
0
Add a random filter subset for BLs (pairwise comparison) for benchmarking
#68
tgattsIV
closed
1 year ago
0
Typo in Phylogenomics Benchmark file name
#67
tgattsIV
closed
1 year ago
1
Tree_Rearrangement step causes memory errors during large data sets in concert with joblib parallelism
#66
tgattsIV
closed
1 year ago
0
Benchmark feature does not take into account when scripts take multiple days
#65
tgattsIV
closed
1 year ago
0
Add a check to Phylogenomics.py to make sure species mapping is working
#64
EvanForsythe
closed
1 year ago
0
added benchmarking features for future script optimization
#63
tgattsIV
closed
1 year ago
0
Add description of benchmarking to readme
#62
EvanForsythe
closed
1 year ago
2
Add logic that supports addending ERC_results file with numbers to avoid filename collisions
#61
tgattsIV
closed
1 year ago
0
Use new benchmarking features to test and optimize regions of bottleneck in ERC Pipeline
#60
tgattsIV
closed
1 year ago
0
Change benchmark folder name
#59
tgattsIV
closed
1 year ago
0
Function decomposition for file verification in mainline script files
#58
tgattsIV
opened
1 year ago
0
Automate dependency install and checksum
#57
tgattsIV
opened
1 year ago
0
Code style and typos
#56
tgattsIV
closed
1 year ago
0
Add benchmarking logfile for upcoming user tests
#55
tgattsIV
closed
1 year ago
0
Erc reformat
#54
tgattsIV
closed
1 year ago
0
Restructure ERC_analyses (and downstream steps)
#53
EvanForsythe
closed
1 year ago
1
added crazy complicated flowchart
#52
EvanForsythe
closed
2 years ago
0
TAPER doesn't work with multi_threads > 1 in mac
#51
EvanForsythe
opened
2 years ago
0
Add taper
#50
EvanForsythe
closed
2 years ago
0
Debug networks
#49
EvanForsythe
closed
2 years ago
0
cleaning up accidentally pushed files/folders
#48
EvanForsythe
closed
2 years ago
0
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