rcastelo/GSVA issues and pull requests

#200 - Store internal GSVA ranks to enable enrichment plots and flexible scoring

Issue - State: open - Opened by rcastelo 10 days ago
Labels: enhancement

#199 - Some

Issue - State: closed - Opened by junglingfish 13 days ago

#198 - Improve messages to the user in annotation mapping and in the GSVA method

Pull Request - State: closed - Opened by rcastelo 19 days ago

#197 - Improve messages to the user

Issue - State: closed - Opened by rcastelo 20 days ago
Labels: enhancement

#196 - matrixStats error

Issue - State: closed - Opened by andreyurch 27 days ago - 1 comment

#195 - New default auto argument to the kcdf parameter in the gsva method

Pull Request - State: closed - Opened by rcastelo 27 days ago

#194 - add annotation mapping for SummarizedExperiment and subclasses

Pull Request - State: closed - Opened by axelklenk 27 days ago
Labels: enhancement

#193 - Add a new default 'auto' argument to the 'kcdf' parameter in the GSVA method

Issue - State: closed - Opened by rcastelo 28 days ago
Labels: enhancement

#192 - Support for GSEA plots

Issue - State: open - Opened by cihanerkut about 1 month ago - 6 comments
Labels: feature request

#188 - How to rewrite? Is there a change in the way GSVA operates?

Issue - State: closed - Opened by lucienhan94 about 1 month ago - 1 comment

#184 - GSVA.so: undefined symbol: match5

Issue - State: closed - Opened by bbimber about 2 months ago - 5 comments

#146 - Error: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').

Issue - State: closed - Opened by BirongZhang 6 months ago - 12 comments

#101 - Why does ssgsea give different values depending on number of samples?

Issue - State: closed - Opened by ahdee about 1 year ago - 1 comment

#100 - Error in .filterFeatures(expr, method): Less than two genes in the input assay object

Issue - State: closed - Opened by bioinformatic-guy about 1 year ago - 3 comments

#99 - modify zscore,not iterate over all cells

Pull Request - State: closed - Opened by Liripo about 1 year ago - 1 comment

#98 - fix oversight in gsvaParam definition causing a Check error

Pull Request - State: closed - Opened by axelklenk about 1 year ago

#97 - 96 gsva method parameter class and constructor

Pull Request - State: closed - Opened by axelklenk about 1 year ago

#96 - GSVA method parameter class and constructor

Issue - State: closed - Opened by axelklenk about 1 year ago
Labels: enhancement

#95 - 85 ssgsea method parameter class and constructor

Pull Request - State: closed - Opened by axelklenk about 1 year ago
Labels: enhancement

#94 - new_api sync to devel, 2nd attempt

Pull Request - State: closed - Opened by axelklenk about 1 year ago - 1 comment
Labels: sync

#93 - new_api sync to devel

Pull Request - State: closed - Opened by axelklenk about 1 year ago - 1 comment
Labels: sync

#92 - How to extract GSVA gene ranking matrix

Issue - State: closed - Opened by cannico30 about 1 year ago - 7 comments

#91 - GSVA() parallelization over multiple node

Issue - State: open - Opened by YouriTasse about 1 year ago - 1 comment
Labels: enhancement

#90 - Error in GSVA() : long vectors not supported in .C

Issue - State: closed - Opened by YouriTasse about 1 year ago - 4 comments
Labels: bug

#89 - NES in ssGSEA

Issue - State: closed - Opened by chunxuan-hs over 1 year ago - 1 comment

#88 - GSVA + SingleCellExperiment: Still experimental?

Issue - State: closed - Opened by llrs over 1 year ago - 1 comment
Labels: bug

#87 - Parametrize feature collinearity detection

Issue - State: closed - Opened by rcastelo over 1 year ago
Labels: bug

#86 - Do I need to scale the scores for comparison?

Issue - State: closed - Opened by aelhossiny over 1 year ago - 1 comment

#85 - ssGSEA method parameter class and constructor

Issue - State: closed - Opened by axelklenk over 1 year ago
Labels: enhancement

#84 - add PLAGE method parameter class and constructor; modify CITATION to …

Pull Request - State: closed - Opened by axelklenk over 1 year ago
Labels: enhancement

#83 - 73 zscore method parameter class and constructor

Pull Request - State: closed - Opened by axelklenk over 1 year ago
Labels: sync

#82 - merge in changes to devel

Pull Request - State: closed - Opened by axelklenk over 1 year ago
Labels: sync

#81 - New API

Issue - State: closed - Opened by axelklenk over 1 year ago - 1 comment
Labels: enhancement

#80 - fix issue #76 by replacing comparisons of class() with calling inheri…

Pull Request - State: closed - Opened by axelklenk over 1 year ago

#79 - fix #77 by adding the missing function call

Pull Request - State: closed - Opened by axelklenk over 1 year ago

#78 - plage method parameter class and constructor

Issue - State: closed - Opened by rcastelo over 1 year ago
Labels: enhancement

#77 - Fixing --as-cran notes on the C code

Issue - State: closed - Opened by rcastelo over 1 year ago - 1 comment
Labels: enhancement

#76 - Fixing --as-cran notes on the R code

Issue - State: closed - Opened by rcastelo over 1 year ago - 2 comments
Labels: enhancement

#75 - There is no package named 'GenomeInfoDbData'.

Issue - State: closed - Opened by ccartermices over 1 year ago - 2 comments

#74 - Error during .mapGeneSetsToFeatures

Issue - State: closed - Opened by rschauner over 1 year ago - 3 comments

#73 - zscore method parameter class and constructor

Issue - State: closed - Opened by rcastelo over 1 year ago - 9 comments
Labels: enhancement

#72 - ssGSEA gave NAN

Issue - State: closed - Opened by FADHLyemen over 1 year ago - 2 comments

#71 - Speed up ssGSEA and reduce memory by moving .fastRndWalk to C++

Issue - State: closed - Opened by rpolicastro over 1 year ago - 3 comments
Labels: enhancement

#70 - why score of single sample change when sample size change per group?

Issue - State: closed - Opened by FADHLyemen over 1 year ago - 4 comments

#69 - Leading edge?

Issue - State: open - Opened by mayanbriller over 1 year ago - 1 comment
Labels: feature request

#68 - Problems with tictoc

Issue - State: closed - Opened by PelzKo over 1 year ago - 4 comments

#67 - Error when runing the function gsva()

Issue - State: closed - Opened by yunbokai over 1 year ago - 7 comments

#66 - Potential discrepancy in ssgsea's implementation

Issue - State: closed - Opened by rached-97 over 1 year ago - 1 comment

#65 - Support for combining scores from directional gene sets

Issue - State: open - Opened by rcastelo almost 2 years ago - 2 comments
Labels: feature request

#64 - An error occurred while running GSVA

Issue - State: closed - Opened by chuiqin about 2 years ago - 3 comments

#62 - The meaning of negative enrichemnt scores resulting from gsva

Issue - State: closed - Opened by charlesgwellem about 2 years ago - 1 comment

#61 - `gsva` with `method='ssgsea'` errors when given a literal single sample

Issue - State: closed - Opened by ChristopherEeles over 2 years ago - 2 comments

#60 - unable to fork, possible reason: Cannot allocate memory when parallel.sz >1

Issue - State: closed - Opened by ditannan over 2 years ago - 2 comments

#59 - Question about the input data and the ssgsea parameters.

Issue - State: closed - Opened by lincj1994 over 2 years ago - 4 comments

#58 - Defunct function

Pull Request - State: closed - Opened by pablo-rodr-bio2 almost 3 years ago

#57 - Question about data input for gsva()

Issue - State: closed - Opened by bieniu777 almost 3 years ago - 2 comments

#56 - how to get the pathways with gene name enriched such as we do in clusterProfiler

Issue - State: closed - Opened by jinaanna almost 3 years ago - 6 comments

#55 - brainTxDbSets genesets in GSVAdata

Issue - State: closed - Opened by kotliary almost 3 years ago - 2 comments

#54 - gsva() causes crash on R v4.1.0

Issue - State: closed - Opened by travis-m-blimkie over 3 years ago - 7 comments