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gabrielodom
/
pathwayPCA
integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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SuperPCA output incongruent with LoadOntoPCs() function
#45
gabrielodom
closed
5 years ago
1
Numerically negative variance output from .coxvar()
#44
gabrielodom
closed
5 years ago
2
SVD fails to converge
#43
gabrielodom
closed
5 years ago
2
'ExtractAESPCs' (and getPathPCLs, SubsetPathwayData) functions lost colnames and rownames
#42
lizhongliu1996
closed
5 years ago
19
function 'CreateOmics' problem
#41
lizhongliu1996
closed
5 years ago
2
PermTest*() Functions fail with ExtractAESPCs() PCs in a data.frame
#40
gabrielodom
closed
5 years ago
1
'ExtractAESPCs' function modify
#39
lizhongliu1996
closed
5 years ago
1
Create Pre-processing functions for Assay and Pathway Collection data
#38
gabrielodom
closed
5 years ago
0
Add "center" and "scale" options at object creation
#37
gabrielodom
closed
5 years ago
6
Filter out features with variance < epsilon
#36
gabrielodom
closed
5 years ago
2
Create a function to load testing data onto PCs by training-data loadings
#35
gabrielodom
closed
5 years ago
0
AESPCA fails to converge
#34
gabrielodom
closed
5 years ago
3
Add warnings and errors to CreateOmics
#33
gabrielodom
closed
5 years ago
3
Combine pathway_tControl and pathway_tScores functions
#32
gabrielodom
closed
5 years ago
1
extract_aesPCS error data undefined cloumn
#31
lizhongliu1996
closed
5 years ago
3
R CMD check fails on Windows but not Mac
#30
gabrielodom
closed
5 years ago
3
Modify the help page of extract_aesPCs
#29
lizhongliu1996
closed
5 years ago
1
Add regression example with PCs and covariates to the vignette
#28
gabrielodom
closed
5 years ago
28
Re-run Ovarian PNNL data with CP:KEGG and C6 Oncogenic Signature
#27
gabrielodom
closed
5 years ago
1
Write data citation paragraph
#26
gabrielodom
closed
5 years ago
2
Standardize Naming Conventions
#25
gabrielodom
closed
5 years ago
5
Removed "expressed" / "expression" from expressedOmes() name and help
#24
gabrielodom
closed
5 years ago
1
Trimmed pathway collections have untrimmed TERMS and description fields
#23
gabrielodom
closed
6 years ago
0
Write "getPathwayData" function
#22
gabrielodom
closed
5 years ago
3
-Omics Class Validity Checks for pathwayCollection Slot
#21
gabrielodom
closed
5 years ago
1
Modify output p-value columns
#20
gabrielodom
closed
5 years ago
2
Messages printed at Pathway Collection Trimming
#19
gabrielodom
closed
6 years ago
1
Create a subsetting function for pathwayCollection-class objects
#18
gabrielodom
closed
5 years ago
5
Replace all mention of "pathwaySet" with "pathwayCollection"
#17
gabrielodom
closed
6 years ago
3
Inspecting top pathways
#16
gabrielodom
closed
5 years ago
12
Add support for set.seed in parallel
#15
gabrielodom
opened
6 years ago
5
Default FDR Adjustment
#14
gabrielodom
closed
6 years ago
1
Generic PCA option
#13
gabrielodom
closed
6 years ago
3
SuperPCA_pVals() Issues
#12
gabrielodom
closed
6 years ago
8
The read_gmt() Function does not remove carriage returns
#11
gabrielodom
closed
6 years ago
1
Add a "write_gmt()" Function
#10
gabrielodom
closed
6 years ago
0
Streamline the `_pVals()` Function Outputs
#9
gabrielodom
closed
6 years ago
7
Supervised PCA function - null density estimation for small number of pathways
#8
gabrielodom
opened
6 years ago
2
Add more realistic data to the package
#7
gabrielodom
closed
6 years ago
4
Add more biological motivation to the current vignettes
#6
gabrielodom
closed
5 years ago
2
Write a new vignette for more experienced R users
#5
gabrielodom
closed
5 years ago
6
Explore the possibility of adding a variance-preservation threshold to the PCA methods
#4
gabrielodom
closed
6 years ago
1
Test faster svd / pca variants
#3
gabrielodom
opened
6 years ago
2
Add "greedy" option to `superpc.st()` function
#2
gabrielodom
closed
6 years ago
1
Run Travis on Bioconductor version
#1
BenBarnard
closed
6 years ago
3
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