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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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cleanup, text notifications added
#114
charles-cowart
closed
1 year ago
3
notebook clean-up
#113
charles-cowart
closed
1 year ago
1
Generate Qiita prep seems to be 16S or other
#112
wasade
opened
1 year ago
4
Minor typo, 394 -> 384
#111
wasade
closed
11 months ago
1
read_plate_map_csv should assert required columns are present
#110
wasade
opened
1 year ago
0
Update metadata_samples_plasmid_sequences.txt
#109
justinshaffer
closed
10 months ago
4
read_plate_map_csv edgecase: numeric samples will be read as numbers
#108
wasade
opened
1 year ago
1
Update calculate_coefficients.py
#107
justinshaffer
closed
10 months ago
0
Update test_rescale_counts.py
#106
justinshaffer
closed
10 months ago
2
Update rescale_counts.py
#105
justinshaffer
closed
10 months ago
1
Update rescale_counts.py
#104
justinshaffer
closed
1 year ago
2
Remove plate_number column from final output
#103
charles-cowart
closed
1 year ago
0
adding metadata.py and tests
#102
sarayupai
closed
10 months ago
1
Removed confusing code + comment
#101
charles-cowart
closed
1 year ago
4
Added option to return prep-file output paths w/study id.
#100
charles-cowart
closed
1 year ago
2
WIP: Fixed empty tm300_8_tool/tm50_8_tool columns.
#99
charles-cowart
closed
1 year ago
2
choices() fix
#98
charles-cowart
closed
1 year ago
0
Spike in Analysis ported from R
#97
dhakim87
closed
1 year ago
2
Adding barcode column to amplicon prep-info-file output
#96
charles-cowart
closed
1 year ago
0
Sample name fix
#95
charles-cowart
closed
1 year ago
0
Sample name fix
#94
charles-cowart
closed
1 year ago
0
fix empty columns in pre-prep
#93
antgonza
closed
1 year ago
0
Modifications based on testing
#92
charles-cowart
closed
1 year ago
0
adding notebooks during install
#91
antgonza
closed
1 year ago
2
prep-info-file generation for amplicon
#90
charles-cowart
closed
1 year ago
2
iSeqnorm pooling notebook.
#89
RodolfoSalido
closed
1 year ago
9
Amplicon support #1
#88
charles-cowart
closed
1 year ago
2
minor changes
#87
antgonza
closed
1 year ago
0
New and unexpected columns in plate metadata.
#86
charles-cowart
closed
1 year ago
2
Modifications based on wet-lab feedback
#85
charles-cowart
closed
1 year ago
0
Input norm + dilution plate functions?
#84
DrCletusSpucklerMD
closed
1 year ago
3
Fix raw_reads column in prep-info output
#83
charles-cowart
closed
10 months ago
2
validate_and_scrub_sample_sheet() function doesn't catch empty 'experiment_design_description' column
#82
RodolfoSalido
closed
6 months ago
0
Create a generalized 'check_against_Qiita' function
#81
charles-cowart
opened
1 year ago
0
Fail validation when sample-sheet contains duplicate entries in [Bioinformatics]
#80
charles-cowart
opened
1 year ago
0
Migrated Wetlab-extensions into metapool package
#79
charles-cowart
closed
2 years ago
3
Added new functions to metagenomics_pipeline_MiniPiconorm jupyter notebook
#78
RodolfoSalido
closed
2 years ago
3
Required columns, prep_columns ideally would come from Qiita
#77
charles-cowart
opened
2 years ago
0
Potential divide/0 errors in calculate_norm_vol()
#76
charles-cowart
opened
2 years ago
1
Prep-file generation now uses sample_name, not well_description.
#75
charles-cowart
closed
2 years ago
0
Update README.md
#74
charles-cowart
opened
2 years ago
0
Update metapool to use sample-names instead of well-descriptions
#73
charles-cowart
closed
2 years ago
0
Adding metatranscriptomics as a valid entry for 'Assay'.
#72
charles-cowart
closed
2 years ago
1
Remove MaskShortReads and OverrideCycles settings for iSeq runs
#71
charles-cowart
closed
2 years ago
2
Add support for metatranscriptomics in samplesheet generator.
#70
RodolfoSalido
closed
2 years ago
2
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
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