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clemente-lab
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mmeds-meta
A database for storing and analyzing omics data
https://mmeds.org
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Make full use of MongoDB for file storage
#470
adamcantor22
opened
6 days ago
0
Bump pymysql from 1.0.2 to 1.1.1
#469
dependabot[bot]
opened
1 month ago
0
Add RandomForest, Lasso, and/or other classifiers to analysis
#468
adamcantor22
opened
3 months ago
0
Enable use in analysis of the ICD code breakdown by parts that is present in database
#467
adamcantor22
opened
3 months ago
0
clarify the structure of analysis directories
#466
adamcantor22
opened
4 months ago
0
mismatch read in strip_error_barcodes
#465
adamcantor22
opened
4 months ago
0
Generate and store sequencing run Qiime artifact immediately after run upload
#464
adamcantor22
opened
5 months ago
0
Additional metadata columns of the same name in subject and specimen files silently fail
#463
adamcantor22
opened
5 months ago
0
Nonstandard dual-barcode lengths break pheniqs
#462
adamcantor22
opened
6 months ago
0
Bump setuptools from 52.0.0 to 65.5.1
#461
dependabot[bot]
closed
4 months ago
3
Allow users to login using email instead of username
#460
adamcantor22
opened
10 months ago
0
Filter out contaminants as default
#459
adamcantor22
opened
10 months ago
0
Bump pygments from 2.8.1 to 2.15.0
#458
dependabot[bot]
closed
4 months ago
2
Migrate "Tools" framework to snakemake workflows
#457
cleme
opened
1 year ago
1
Enhancement previous changes
#456
adamcantor22
closed
9 months ago
1
Organize minerva studies by user
#455
adamcantor22
opened
1 year ago
0
Fix config examples
#454
adamcantor22
opened
1 year ago
0
Update user docs
#453
adamcantor22
opened
1 year ago
0
Standardize drug names
#452
jakleenlee
opened
1 year ago
0
Metadata subclasses and conversion
#451
adamcantor22
opened
1 year ago
2
define metadata ontologies
#450
adamcantor22
opened
1 year ago
0
expand options in analysis tool configurations
#449
adamcantor22
opened
1 year ago
0
updated conda env, fixed issue with no discrete metadata columns
#448
mstapylton
closed
1 year ago
1
Improved summaries: refactor summary code out of generated jupyter notebooks into MMEDs and improve summary code overall
#447
mstapylton
opened
1 year ago
0
issue with how summary for study adamcantor22_Nasal_Swabs_Microbiome_S_0 was generated
#446
mstapylton
closed
1 year ago
0
Bump pillow from 8.3.2 to 9.3.0
#445
dependabot[bot]
closed
1 year ago
2
Consider adding UMAP analysis
#444
cleme
opened
1 year ago
1
Add rPCA analysis
#443
cleme
opened
1 year ago
0
Studies with mixed data types
#442
cleme
opened
1 year ago
0
Adding studies MMEDS
#441
cleme
opened
1 year ago
0
Re-establish a way to auto-submit jobs on the server
#440
adamcantor22
opened
1 year ago
1
expand options for rarefaction/depth values
#438
adamcantor22
opened
1 year ago
0
add options for demultiplexing single barcodes
#437
adamcantor22
opened
1 year ago
0
Checks and info on uploaded sequencing runs
#436
adamcantor22
opened
1 year ago
0
remove vulnerabilities
#435
adamcantor22
closed
1 year ago
0
Improve time complexity of meta analysis queries
#434
adamcantor22
opened
1 year ago
0
Refactor util.py
#433
adamcantor22
opened
1 year ago
0
Dedicated Metadata Class
#432
adamcantor22
opened
1 year ago
3
Remove old sub-analysis functionality and re-integrate as a variant of meta-analysis
#431
adamcantor22
opened
1 year ago
0
Proper cropping of LEfSe output SVGs
#430
cleme
opened
1 year ago
1
Enhancement meta analysis
#429
adamcantor22
closed
1 year ago
1
Organization of data and metadata
#428
cleme
opened
1 year ago
0
Investigate recent features once web01 comes back online
#427
adamcantor22
closed
1 year ago
1
Improve mmeds file pathing
#426
adamcantor22
opened
1 year ago
0
Enhancement adding analysis tools
#425
adamcantor22
closed
1 year ago
1
Investigate LEfSe normalization
#424
adamcantor22
closed
1 year ago
3
Future Issues - Meta
#423
adamcantor22
opened
1 year ago
0
Improved summaries: correct recognition of dates as continuous variables
#422
adamcantor22
opened
1 year ago
1
Issue fix consistent validation
#421
adamcantor22
closed
1 year ago
1
Minor inconsistency bugs in validation and analysis
#420
adamcantor22
closed
1 year ago
0
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