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audy
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richardson-2014
Analysis code for the DIPP microbiome study
http://dipp.utu.fi
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Problems with normalize.R
#57
adriaaula
opened
8 years ago
1
update w/ audy branch for publication
#56
audy
closed
9 years ago
0
pca ~ diversity index
#55
audy
closed
10 years ago
1
Calculate values for columns in sample data based on values of other columns
#54
audy
closed
10 years ago
0
add packrat files
#53
audy
closed
10 years ago
0
Generate random names for subjects to make it easier to discuss/remember them.
#52
audy
closed
10 years ago
0
Use dplyr in place of plyr
#51
audy
opened
10 years ago
0
Use data.table for loading CSV files (because they're quite large).
#50
audy
closed
10 years ago
1
Combine Genus and species names in species-level plots.
#49
audy
closed
10 years ago
0
Add figure theme
#48
audy
closed
10 years ago
1
Add appearance of autoantibodies to time-series plots
#47
audy
closed
10 years ago
0
Add GLM to time-series analysis
#46
audy
closed
10 years ago
0
Plot ROC curve for GLM
#45
audy
closed
10 years ago
0
Gmulti
#44
audy
closed
10 years ago
0
Add qPCR GLM regression
#43
audy
closed
10 years ago
0
Fix scales in sliding window plots
#42
audy
closed
10 years ago
0
Add linear regression and calculate R^2 for diversity measures plot
#41
audy
opened
10 years ago
0
Sliding window diversity
#40
audy
closed
10 years ago
0
The real sliding window
#39
audy
closed
10 years ago
0
Remove (possibly) contaminated samples?
#38
audy
closed
10 years ago
1
Re-assign taxonomies
#37
audy
closed
10 years ago
0
Comply with the MIMARKS
#36
audy
closed
10 years ago
1
Sample Barcode Mapping
#35
audy
closed
10 years ago
0
Sample Barcode Mapping
#34
audy
closed
10 years ago
2
Sliding window ordination
#33
audy
closed
10 years ago
0
Run sequences through QIIME 1.8
#32
audy
closed
10 years ago
0
Independent surrogate variable analysis
#31
audy
closed
10 years ago
1
Comply with LGPL for qvalue code
#30
audy
closed
10 years ago
0
Normalize using Total Bacterial Count
#29
audy
closed
10 years ago
1
Do non time-series hypothesis testing.
#28
audy
closed
10 years ago
1
Add test data
#27
audy
opened
10 years ago
0
Closes #24
#26
audy
closed
10 years ago
0
Do actual SLIDING window smoothing/hypothesis testing
#25
audy
closed
10 years ago
0
Fix qvalue calculation to use the # of OTUs not # OTUs * # Samples
#24
audy
closed
10 years ago
0
Add FDR Corrections
#23
audy
closed
10 years ago
0
Generate biom files
#22
audy
opened
10 years ago
0
Add code to generate Wiggum plots
#21
audy
closed
10 years ago
1
closes #18
#20
audy
closed
10 years ago
0
Download PICRUST precalc files in Makefile
#19
audy
closed
10 years ago
1
Correct for copy number variation
#18
audy
closed
10 years ago
0
Incorporate GLMULTI code
#17
audy
closed
10 years ago
1
Resolves #14
#16
audy
closed
10 years ago
0
Plot ordination
#15
audy
closed
10 years ago
0
Load/Save phylogenetic tree
#14
audy
closed
10 years ago
1
Add ordination plots
#13
audy
closed
10 years ago
1
Add GreenGenes 97% Rep Set Tree
#12
audy
closed
10 years ago
1
PERMANOVA time series code.
#11
audy
closed
10 years ago
1
Added Picrust
#10
audy
closed
10 years ago
0
Add FDR corrections
#9
audy
closed
10 years ago
5
Add PICRUST code
#8
audy
closed
10 years ago
0
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