audy richardson-2014 issues

audy / richardson-2014

Analysis code for the DIPP microbiome study

http://dipp.utu.fi

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issues

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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