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BeeCSI-Microbiome
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R_analyses
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Major update
#34
LLansing
closed
1 year ago
0
Fix additional_taxa assignment for datasets with multiple additional taxa
#33
LLansing
opened
1 year ago
0
Kurt cleanup
#32
Kurtj-hub
closed
1 year ago
1
Changes discussed earlier today mostly implemented
#31
Kurtj-hub
closed
1 year ago
0
Refactoring lance fall 2022
#30
LLansing
closed
1 year ago
0
Refactoring lance fall 2022
#29
LLansing
closed
1 year ago
0
Look into writing test statistics and indicSpecies results as csv files in addition to the current txt output
#28
LLansing
opened
1 year ago
3
Refactoring lance fall 2022
#27
LLansing
closed
1 year ago
0
Determine the fate of fitZig DA analysis
#26
LLansing
closed
1 year ago
1
Update and review README and documentation
#25
LLansing
opened
1 year ago
0
Clarify in all output files what taxa level is represented
#24
LLansing
opened
2 years ago
0
Clarify in output files that only Bacterial reads remain after filtering
#23
LLansing
opened
2 years ago
0
Optimization kurt
#22
Kurtj-hub
closed
1 year ago
1
Update initial_processing.R
#21
Kurtj-hub
closed
2 years ago
2
ANCOMBC doesn't correctly adjust p-value when there is more than 1 contrast (i.e. 3 or more treatments)
#20
LLansing
opened
2 years ago
1
Add back in css_percentile
#19
LLansing
closed
2 years ago
0
Fix to work with Pavian script formatted count tables
#18
LLansing
closed
2 years ago
0
Integrate ancombc into main.R
#17
jonathho
closed
2 years ago
0
Modify fold change to be log base 2 instead of base e
#16
jonathho
closed
2 years ago
1
Change Natural logarithm in x-axis of volcano plot to base2 logarithm
#15
ropolomx
closed
2 years ago
3
Merge Differential abundance with main
#14
LLansing
closed
2 years ago
0
Merge Kurt's DA integration branch with DA
#13
LLansing
closed
2 years ago
0
Activity 2 nmds
#12
jonathho
closed
2 years ago
0
Refactoring
#11
jonathho
closed
2 years ago
0
Implement minimum count filter
#10
LLansing
opened
2 years ago
2
Implement filtering to only Bacteria (no eukaryotes)
#9
LLansing
closed
2 years ago
0
Handle "unclassified X"
#8
LLansing
closed
2 years ago
2
Reimplement Clade Count Calculation for better time complexity
#7
LLansing
opened
2 years ago
2
Jonathho patch 1
#6
jonathho
closed
2 years ago
0
Differential abundance
#5
ropolomx
opened
2 years ago
2
Implement renv to keep software versions consistent
#4
ropolomx
opened
2 years ago
1
Organize the target modules
#3
ropolomx
opened
2 years ago
3
[WIP] Document workflow from raw data to analyses
#1
ropolomx
closed
2 years ago
0