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biocore
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metagenomics_pooling_notebook
Jupyter notebooks to assist with sample processing
MIT License
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validate qiita sample names in read_plate_map_csv
#69
antgonza
closed
2 years ago
0
WarningMessages and quiet_validate_and_scrub_sample_sheet()
#68
charles-cowart
opened
2 years ago
0
OverrideCycles is invalid for iSeq
#67
wasade
closed
2 years ago
7
Update error text for parsing run ID
#66
wasade
closed
2 years ago
4
Add iseq
#65
wasade
closed
2 years ago
1
Confirm/Verify that the notebooks requiere center_name and experiment_design_description
#64
antgonza
opened
2 years ago
1
Removed qiita_id from prep-file output
#63
charles-cowart
closed
2 years ago
0
Notebook reorganization
#62
kfogelso
closed
2 years ago
6
Created notebooks folder and moved notebooks, test_data and test_output into subfolder
#61
kfogelso
closed
2 years ago
1
Validate sample sheets before merging
#60
ElDeveloper
opened
2 years ago
0
parsefier.astype
#59
antgonza
closed
2 years ago
1
Fix negative plate reader concentration handling
#58
RodolfoSalido
closed
2 years ago
9
Negative concentrations from SpectraMax_i3x reader output break normalization functions.
#57
RodolfoSalido
closed
1 year ago
3
Amplicon prep fix
#56
charles-cowart
closed
2 years ago
10
Add notes to notebook about file extensions
#55
ElDeveloper
closed
5 months ago
0
Reorder columns in amplicon prep
#54
ElDeveloper
closed
2 years ago
2
Add run id and instrument model to amplicon preps
#53
ElDeveloper
opened
2 years ago
0
Remove forward and reverse adapters for amplicon notebook
#52
ElDeveloper
opened
2 years ago
0
Added references to __init__.py
#51
charles-cowart
closed
2 years ago
0
ENH: Add a quiet variant of the sample sheet validation
#50
ElDeveloper
closed
2 years ago
0
ENH: Add well description generation
#49
ElDeveloper
closed
2 years ago
1
wip. do not merge.
#48
charles-cowart
closed
2 years ago
0
BUG: Remove Experiment key from notebooks
#47
ElDeveloper
closed
2 years ago
0
SampleSheet generator module runs with warnings. Well_description column broken.
#46
RodolfoSalido
closed
2 years ago
3
Add filename generator for sample sheet and preparation file
#45
ElDeveloper
opened
2 years ago
1
Bclconvert
#44
charles-cowart
closed
2 years ago
5
Bcl convert
#43
charles-cowart
closed
2 years ago
0
Created notebooks folder & minor updates
#42
kfogelso
closed
2 years ago
3
Add MaskShortReads and OverrideCycles to Settings section
#41
ElDeveloper
closed
2 years ago
7
Generate amplicon mapping (prep) files with metapool/scripts/seqpro.py
#40
ElDeveloper
opened
2 years ago
4
Updated read_plate_map_csv to fail with repeated sample names
#39
cguccione
closed
2 years ago
16
18S and ITS updates
#38
callaband
closed
2 years ago
4
ENH: Change column names for count collector
#37
ElDeveloper
closed
2 years ago
1
re Issue #23: adds fields for library_construction_protocol and experiment_design_description
#36
ahdilmore
closed
2 years ago
7
Collect sequence counts during prep file generation
#35
ElDeveloper
closed
2 years ago
1
Explore the feasibility of porting notebooks to use Jupyter widgets
#34
ElDeveloper
opened
2 years ago
0
Add some dependencies in the conda environment
#33
ElDeveloper
closed
2 years ago
0
Revert "Add support for parsing sample sheets with empty lines"
#32
charles-cowart
closed
2 years ago
2
Update README installation instructions to recommend conda for dependencies with binaries
#31
ElDeveloper
closed
2 years ago
1
Tag a release
#30
ElDeveloper
opened
2 years ago
0
Add support for 18S and ITS in amplicon-pooling.ipynb
#29
ElDeveloper
closed
2 years ago
0
Update metapool.prep.preparations_for_run to work with 16S data
#28
ElDeveloper
opened
2 years ago
0
Cleanup iTru index combo generator
#27
ElDeveloper
opened
2 years ago
2
Add gDNA concentration check (dilution) function
#26
RodolfoSalido
closed
1 year ago
1
Add test data for all notebooks
#25
ElDeveloper
closed
5 months ago
0
Move notebooks and test data to a different directory.
#24
ElDeveloper
closed
5 months ago
0
Add a field for library_construction_protocol and experiment_design_description
#23
ElDeveloper
closed
2 years ago
1
Change read_plate_map_csv to fail with repeated sample names
#22
ElDeveloper
closed
2 years ago
0
Add support for parsing sample sheets with empty lines
#21
ElDeveloper
closed
2 years ago
3
Add new plate reader compatibility. Update REVCOMP_SEQUENCERS
#20
RodolfoSalido
closed
2 years ago
1
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