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biocore
/
oecophylla
shotgun pipeline
MIT License
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added SHOGUN functional profiling
#116
qiyunzhu
closed
6 years ago
5
updated diamond db version to 8.36
#115
tanaes
closed
6 years ago
0
added back in bowtie test db
#114
tanaes
closed
6 years ago
0
shogun conda environment messes up environment variables
#113
qiyunzhu
closed
6 years ago
1
Updated documentation for new installs and tests
#112
tanaes
closed
6 years ago
1
Taxonomy fixes
#111
tanaes
closed
6 years ago
3
Improve launch script
#110
tanaes
closed
6 years ago
2
Adding in another skeleton for install within the launch script
#109
mortonjt
closed
6 years ago
0
Distance.rule optimization
#108
mortonjt
opened
6 years ago
1
added Centrifuge and SHOGUN test databases
#107
qiyunzhu
closed
6 years ago
4
addressed issue #104
#106
qiyunzhu
closed
6 years ago
0
Shogun test_db needs metadata.yaml
#105
tanaes
closed
6 years ago
1
Taxonomy-centrifuge needs env install added to taxonomy.sh
#104
tanaes
closed
6 years ago
1
Fixes to Distance module
#103
tanaes
closed
6 years ago
6
Fix some small config errors
#102
tanaes
closed
6 years ago
3
Initial Barnacle release
#101
tanaes
opened
6 years ago
0
Added Centrifuge rule
#100
qiyunzhu
closed
6 years ago
7
Fix humann2 rule
#99
tanaes
closed
6 years ago
2
Improve launch script
#98
tanaes
closed
6 years ago
2
Improve launch script
#97
tanaes
closed
6 years ago
1
cleaned up test database locations
#96
tanaes
closed
6 years ago
1
Re-estimate per-rank abundance based on Centrifuge result
#95
qiyunzhu
closed
6 years ago
1
Translate MetaPhlAn2 taxonomy terms back to NCBI TaxIDs
#94
qiyunzhu
closed
6 years ago
3
Translate SHOGUN taxonomy terms back to NCBI TaxIDs
#93
qiyunzhu
opened
6 years ago
2
upgraded Metaphlan2 rule
#92
qiyunzhu
closed
6 years ago
23
merged raw rules into qc module
#91
tanaes
closed
6 years ago
4
updating dev
#90
mortonjt
closed
6 years ago
1
Improved SHOGUN rule
#89
qiyunzhu
closed
6 years ago
2
Improved Kraken / Bracken rules
#88
qiyunzhu
closed
6 years ago
1
a new function to write a Pandas.DataFrame into a biom file
#87
sjanssen2
closed
6 years ago
1
Config.yaml shouldn't be regenerated for every run
#86
mortonjt
closed
6 years ago
1
Unit tests
#85
sjanssen2
opened
6 years ago
2
Fixed the MetaPhlAn2 database parameter broken issue in #82
#84
qiyunzhu
closed
6 years ago
1
Bracken installation code not working in Travis
#83
qiyunzhu
closed
6 years ago
3
Added SHOGUN support
#82
qiyunzhu
closed
6 years ago
5
Add taxonomic profiling tools' options to config.yaml
#81
qiyunzhu
closed
6 years ago
2
Make DAGs for documentation
#80
tanaes
opened
7 years ago
0
added Philosophy (overview) section
#79
cuttlefishh
closed
6 years ago
2
ENH: add positional argument support to the launch script
#78
tkosciol
closed
6 years ago
1
Launch script
#77
mortonjt
closed
6 years ago
6
Add Centrifuge to taxonomy
#76
tanaes
closed
6 years ago
1
Assets
#75
wasade
closed
7 years ago
0
add sourmash rules
#74
RNAer
closed
7 years ago
2
Switching to a single filter db for all samples
#73
tanaes
closed
7 years ago
3
adding a Phyton function to combine individual bracken output into on…
#72
sjanssen2
closed
6 years ago
3
Combine bracken
#71
sjanssen2
closed
7 years ago
0
Added Bracken support
#70
qiyunzhu
closed
7 years ago
4
added Bracken support
#69
qiyunzhu
closed
7 years ago
1
Need to have filtering be an explicit params in Snakefile
#68
mortonjt
closed
6 years ago
2
WIP: launch script skeleton
#67
tkosciol
closed
7 years ago
2
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