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krumsieklab
/
maplet
R statistical toolbox for metabolomics
GNU General Public License v3.0
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SGI
#71
KelseyChetnik
closed
1 year ago
2
Pairing functionality for boxplots
#70
KelseyChetnik
opened
3 years ago
1
Add fixed seed to non-deterministic functions
#69
KelseyChetnik
closed
3 years ago
2
Barchart with errorbars
#68
KelseyChetnik
opened
3 years ago
0
Pathway enrichment analysis
#67
KelseyChetnik
opened
3 years ago
1
Load Metabolon files: use metabolite names instead of Metabolon id as assay rownames
#66
KelseyChetnik
closed
3 years ago
7
make function to add metabolite/sample missingness percentage as a rowData/colData column
#65
KelseyChetnik
closed
3 years ago
3
add a function that converts different metabolite IDs given a lookup table
#64
KelseyChetnik
opened
3 years ago
1
Network-based ratios
#63
KelseyChetnik
closed
3 years ago
2
Add optional double axis to missingness plots (percentage + numbers)
#62
KelseyChetnik
closed
3 years ago
2
Updated KEGG annotations
#61
KelseyChetnik
opened
3 years ago
0
Find a way to integrate aggregation into non-aggregation pipelines, or general non-linear pipelines, or multiple pipelines for the RMD.
#60
KelseyChetnik
closed
3 years ago
2
PCA: check that all coloring input fields really exist
#59
KelseyChetnik
closed
3 years ago
2
Lasso / glm type of multivariable methods
#58
KelseyChetnik
opened
3 years ago
3
Heatmap plot showing results of multiple statistics at the same time
#57
KelseyChetnik
closed
3 years ago
4
mt_verify...
#56
KelseyChetnik
closed
3 years ago
1
p-value brackets on boxplots and barplots
#55
KelseyChetnik
closed
3 years ago
1
Get rid of all warning messages that occur during a pipeline run.
#54
KelseyChetnik
closed
3 years ago
1
Check collinearity in input data
#53
KelseyChetnik
closed
3 years ago
1
Barchart with errorbars
#52
KelseyChetnik
closed
3 years ago
1
Compact Boxplots
#51
KelseyChetnik
closed
3 years ago
1
Automatically determine if data is logged
#50
KelseyChetnik
closed
3 years ago
2
Missingness plots: Sample-wise sorted missingness
#49
KelseyChetnik
closed
3 years ago
1
Tests for normality
#48
KelseyChetnik
closed
3 years ago
1
sparse PCA for feature reduction
#47
KelseyChetnik
closed
3 years ago
1
lasso / glm type of multivariable methods
#46
KelseyChetnik
closed
3 years ago
1
Document logging functionality properly
#45
KelseyChetnik
closed
3 years ago
1
add our lab affiliation to all of the roxygens
#44
KelseyChetnik
closed
3 years ago
1
get rid of 'metabolite' everywhere
#43
KelseyChetnik
closed
3 years ago
1
todo: network-based ratios
#42
KelseyChetnik
closed
3 years ago
1
Network overlap functions, reference comparison
#41
KelseyChetnik
closed
3 years ago
2
combat function should crash if there's NAs in the data matrix
#40
KelseyChetnik
closed
3 years ago
2
Transfer conventions into markdown
#39
KelseyChetnik
closed
3 years ago
1
todo: very slim boxplot implementation for sample boxplot
#38
KelseyChetnik
closed
3 years ago
1
bug: missing value function crashes with missing values
#37
KelseyChetnik
closed
3 years ago
1
volcano plot: add option to filter by log fold change
#36
KelseyChetnik
closed
3 years ago
2
todo: add functionality to transform metabolites >x% missingness into binary variables (present/absent)
#35
KelseyChetnik
closed
3 years ago
2
mt_pre_outlier: outlier_ variable should be logical
#34
KelseyChetnik
closed
3 years ago
1
todo: Key Pathway Miner functionality (i.e. ORA type of Modentify)
#33
KelseyChetnik
closed
3 years ago
1
todo: Pathifier algorithm
#32
KelseyChetnik
closed
3 years ago
1
todo: WGCNA functionality
#31
KelseyChetnik
closed
3 years ago
1
todo: fix logging strings of equation terms (e.g. volcano plot)
#30
KelseyChetnik
closed
3 years ago
1
todo: Transform dataset into PCs (without pathways)
#29
KelseyChetnik
closed
3 years ago
1
todo: tester functions, verifying that all methods behave correctly
#28
KelseyChetnik
closed
3 years ago
1
todo: all against all omics
#27
KelseyChetnik
closed
3 years ago
1
todo: metabolite distribution plot across samples
#26
KelseyChetnik
closed
3 years ago
1
todo: mean vs. sample plot
#25
KelseyChetnik
closed
3 years ago
1
todo: ratio maker - complex version
#24
KelseyChetnik
closed
3 years ago
1
todo: general plotting functions to compare sample attributes
#23
KelseyChetnik
closed
3 years ago
1
todo: PredRank (extension of SurvRank)
#22
KelseyChetnik
closed
3 years ago
1
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