danknights mwas issues - Githubissues

danknights / mwas

Perform microbiome-wide association studies with a variety of models

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Question: Link for paper?

#25 complexgenome opened 7 years ago
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command-line script for predicting using trained model

#24 danknights closed 9 years ago
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Clean up beeswarm/violin plot code for command-line use

#23 danknights opened 10 years ago
1
Clean up heatmap code for command-line use

#22 danknights opened 10 years ago
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Clean up linear and mixed linear stats tests for command line use

#21 danknights opened 10 years ago
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write export code (and determine format)

#20 danknights closed 9 years ago
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Add feature selection using random forests

#19 danknights closed 10 years ago
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add glmnet classifier

#18 danknights closed 10 years ago
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Use Kernlab import and use unifrac for SVM

#17 danknights closed 9 years ago
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Look into S3-level objects for modularity

#16 danknights closed 9 years ago
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Output probability from random forests, knn, log. regression, svm, etc.

#15 danknights closed 9 years ago
1
Model evaluation measure: Cohen's Kappa

#14 danknights closed 10 years ago
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Model evaluation measure: MCC (matthew's correlation coefficient)

#13 danknights closed 10 years ago
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Model evaluation measure: AUC (for models that output probability)

#12 danknights closed 10 years ago
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Model evaluation measure: classwise/normal accuracy

#11 danknights closed 10 years ago
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Wrapper method use jackknifing/cross-validation for std. dev. of error

#10 danknights closed 9 years ago
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Train final model on whole data set

#9 danknights closed 9 years ago
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Allow input of classic OTU table or taxon table

#8 danknights closed 10 years ago
1
Make beeswarm plots fit large labels on x axis

#7 danknights closed 10 years ago
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Make quantiles optional

#6 danknights opened 10 years ago
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add function to parse QIIME PCoA file

#5 danknights opened 10 years ago
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Add function to subset data

#4 danknights opened 10 years ago
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use qiimeio for txt-format and biom packages for IO

#3 danknights closed 10 years ago
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plot_gradients.r should also plot pcoa by discrete/continuous metadata

#2 danknights opened 10 years ago
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plot_gradients.r fails when shortening taxonomy on some input files

#1 danknights opened 10 years ago
0