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rcastelo
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GSVA
Gene set variation analysis
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Number of pathway output
#154
Chrisdoan9
closed
6 months ago
5
Implementing new wrapData() and unwrapData() methods for SpatialExper…
#153
peremoles
closed
6 months ago
1
Implement random walk for spot data
#152
rcastelo
closed
6 months ago
0
disable explicit sparse-to-dense coercion when unwrapping …
#151
axelklenk
closed
6 months ago
0
Implementing new wrapData() and unwrapData() methods
#150
peremoles
closed
6 months ago
0
Add SpatialExperiment class
#149
peremoles
closed
6 months ago
0
Support for spatial transcriptomics data
#148
rcastelo
opened
6 months ago
0
Add SpatialExperiment class to the gsvaExprData union class
#147
rcastelo
closed
6 months ago
0
Error: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
#146
BirongZhang
closed
4 months ago
12
Sparse-to-dense coercion of sparse matrices in SummarizedExperiment and/or SingleCellExperiment
#145
axelklenk
closed
6 months ago
0
Running GSVA without kernel density estimation on a dgCMatrix coerces to a dense matrix
#144
axelklenk
closed
2 months ago
0
make resulting ES matrices always dense
#143
axelklenk
closed
7 months ago
0
Gene set expression score matrices are not sparse
#142
axelklenk
closed
7 months ago
0
loading gsva causing R to encounter fatal error
#141
rg510
closed
6 months ago
2
add a nice gsvaShow() method for displaying dgCMatrix objects that ar…
#140
axelklenk
closed
7 months ago
0
improve show method for parameter objects when data matrix is a dgCMatrix
#139
axelklenk
closed
7 months ago
0
re-implement gene filtering without using floating point arithmetic for both dense and sparse matrices
#138
axelklenk
closed
7 months ago
0
Help with Error in gsvaParam(X, gs) : could not find function "gsvaParam"
#137
Chrisdoan9
closed
7 months ago
10
Abs value of the rank?
#136
xpeng-26
closed
7 months ago
1
Questions about the parameter "ssgsea.norm" of ssGSEA
#135
HMU-WH
closed
7 months ago
2
122 moving package documentation to roxygen2
#134
axelklenk
closed
8 months ago
0
gsva error
#133
tcmlab
closed
8 months ago
4
131 modify signatures of gsva generic and methods for new api
#132
axelklenk
closed
9 months ago
0
modify signatures of gsva() generic and methods for new API
#131
axelklenk
closed
9 months ago
0
move old API from deprecated to defunct
#130
axelklenk
closed
9 months ago
0
move old API from deprecated to defunct
#129
axelklenk
closed
9 months ago
0
move igsva() Shiny app to new API; fix two UI buglets
#128
axelklenk
closed
9 months ago
0
Move Shiny app to new API
#127
axelklenk
closed
9 months ago
0
121 refactoring code of the internal implementation of gsva methods
#126
axelklenk
closed
9 months ago
0
for each GSVA analysis method, add an R script and expected output
#125
axelklenk
closed
10 months ago
0
Regression testing for detecting unintended side effects of internal code refactoring
#124
axelklenk
closed
10 months ago
0
GSVAparam error
#123
akettring
closed
10 months ago
2
Moving package documentation to roxygen2
#122
rcastelo
closed
8 months ago
0
Refactoring code of the internal implementation of GSVA methods
#121
rcastelo
closed
9 months ago
0
New api
#120
axelklenk
closed
11 months ago
1
New api
#119
axelklenk
closed
11 months ago
0
show() methods for parameter objects
#118
axelklenk
closed
11 months ago
0
add show() methods for parameter objects that re-use components' show…
#117
axelklenk
closed
11 months ago
0
add show() methods for parameter objects that re-use components' show…
#116
axelklenk
closed
11 months ago
0
Update GSVA vignette
#115
rcastelo
opened
1 year ago
0
Unit tests for annotation features
#114
rcastelo
opened
1 year ago
3
Use of the dgCMatrix container
#113
rcastelo
opened
1 year ago
4
Use of the SingleCellExperiment container
#112
rcastelo
opened
1 year ago
0
New API for GSVA based on method-specific parameter objects
#111
axelklenk
closed
1 year ago
1
migrate vignette to new API; work around eSet/annotation() problem
#110
axelklenk
closed
1 year ago
0
add slots and constructor arguments for 'annotation', 'minSize', and …
#109
axelklenk
closed
1 year ago
0
Add argument 'assay' to parameter objects to make example(gsva) work.
#108
axelklenk
closed
1 year ago
0
add code and docs for deprecation of old interface; add docs for new …
#107
axelklenk
closed
1 year ago
0
New API -- now including man/*.Rd files
#106
axelklenk
closed
1 year ago
0
New API implementation as discussed
#105
axelklenk
closed
1 year ago
0
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