lgeistlinger/enrichmentbrowser issues and pull requests

#52 - Add support for obtaing gene sets from rummagene

Issue - State: closed - Opened by lgeistlinger 7 months ago - 1 comment
Labels: enhancement

#51 - EnrichmentBrowser and scRNA-seq data - how to?

Issue - State: open - Opened by tim-meese 8 months ago - 1 comment
Labels: question

#50 - Error running topologygsa: is.DAG(gr) throwing "Input must be a matrix or a dgCMatrix"

Issue - State: open - Opened by ChangqingW 8 months ago
Labels: bug

#49 - Error in .org2pkg(anno): unrecognized organism ID 'mcf'

Issue - State: open - Opened by Shi-YuZhang about 1 year ago - 1 comment
Labels: question

#48 - Error in `collect()`: ! Failed to collect lazy table.

Issue - State: closed - Opened by Shi-YuZhang about 1 year ago - 2 comments

#47 - Can Enrichment Browser use fgsea

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

#46 - NetGSA no longer works

Issue - State: open - Opened by cpuritz over 1 year ago
Labels: bug

#45 - getGenesets returns a list of empty named lists when calling mice KEGG genesets

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

#44 - Enrichmentbrowser rmd

Pull Request - State: closed - Opened by Rohit-Satyam about 2 years ago - 12 comments

#43 - Vignette Conversation Request

Issue - State: closed - Opened by Rohit-Satyam about 2 years ago - 2 comments

#42 - Fix bug in '.getMSigDB' function

Pull Request - State: closed - Opened by vdsukhov over 3 years ago - 5 comments

#41 - error with eaBrowse

Issue - State: closed - Opened by ZHIDIHUAYUAN over 3 years ago - 6 comments
Labels: bug

#40 - Running deAna() using decimal (non-integer) counts with DESeq2 method

Issue - State: closed - Opened by haghshenas over 3 years ago - 5 comments

#40 - Running deAna() using decimal (non-integer) counts with DESeq2 method

Issue - State: closed - Opened by haghshenas over 3 years ago - 5 comments

#39 - Function and KEGG species id not working

Issue - State: closed - Opened by Fuad59 almost 4 years ago - 8 comments

#39 - Function and KEGG species id not working

Issue - State: closed - Opened by Fuad59 almost 4 years ago - 8 comments

#38 - Support for plots from the enrichplot package?

Issue - State: open - Opened by jorainer almost 4 years ago - 2 comments
Labels: enhancement

#38 - Support for plots from the enrichplot package?

Issue - State: open - Opened by jorainer almost 4 years ago - 2 comments
Labels: enhancement

#37 - Compatibility with MSigDB 7.2

Issue - State: closed - Opened by GabrielHoffman almost 4 years ago - 2 comments

#37 - Compatibility with MSigDB 7.2

Issue - State: closed - Opened by GabrielHoffman almost 4 years ago - 2 comments

#36 - KEGG gene set names are inconsiset

Issue - State: closed - Opened by GabrielHoffman almost 4 years ago - 2 comments

#36 - KEGG gene set names are inconsiset

Issue - State: closed - Opened by GabrielHoffman almost 4 years ago - 2 comments

#35 - Option for hierarchical definition of GO gene sets

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 1 comment
Labels: enhancement

#35 - Option for hierarchical definition of GO gene sets

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 1 comment
Labels: enhancement

#34 - Why is GAGE not an implemented method?

Issue - State: closed - Opened by tmms1 about 4 years ago - 2 comments
Labels: question

#34 - Why is GAGE not an implemented method?

Issue - State: closed - Opened by tmms1 about 4 years ago - 2 comments
Labels: question

#33 - Integrating getGenesets with idMap

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 3 comments
Labels: enhancement

#33 - Integrating getGenesets with idMap

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 3 comments
Labels: enhancement

#32 - caching recalls wrong object type

Issue - State: closed - Opened by GabrielHoffman about 4 years ago - 4 comments
Labels: enhancement

#32 - caching recalls wrong object type

Issue - State: closed - Opened by GabrielHoffman about 4 years ago - 4 comments
Labels: enhancement

#31 - getGenesets fails with enrichr

Issue - State: closed - Opened by GabrielHoffman about 4 years ago - 3 comments
Labels: bug

#31 - getGenesets fails with enrichr

Issue - State: closed - Opened by GabrielHoffman about 4 years ago - 3 comments
Labels: bug

#30 - Issue loading MSigDB

Issue - State: closed - Opened by GabrielHoffman about 4 years ago - 2 comments

#30 - Issue loading MSigDB

Issue - State: closed - Opened by GabrielHoffman about 4 years ago - 2 comments

#29 - import: experimental designs with more than one covariate

Issue - State: open - Opened by lgeistlinger about 4 years ago
Labels: enhancement

#29 - import: experimental designs with more than one covariate

Issue - State: open - Opened by lgeistlinger about 4 years ago
Labels: enhancement

#28 - Multiple factor experiments (non-binary).

Issue - State: open - Opened by grabearummc about 4 years ago - 6 comments
Labels: enhancement

#28 - Multiple factor experiments (non-binary).

Issue - State: open - Opened by grabearummc about 4 years ago - 6 comments
Labels: enhancement

#27 - How can I make use of DESeq2's normalization factors during import?

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 1 comment
Labels: enhancement

#27 - How can I make use of DESeq2's normalization factors during import?

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 1 comment
Labels: enhancement

#26 - Import from limma-trend approach

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 2 comments
Labels: enhancement

#26 - Import from limma-trend approach

Issue - State: closed - Opened by lgeistlinger about 4 years ago - 2 comments
Labels: enhancement

#25 - Error catching with new import function.

Issue - State: closed - Opened by grabearummc about 4 years ago - 3 comments
Labels: enhancement

#25 - Error catching with new import function.

Issue - State: closed - Opened by grabearummc about 4 years ago - 3 comments
Labels: enhancement

#24 - ENSEMBL ID version conversion

Issue - State: closed - Opened by grabear about 4 years ago - 9 comments

#24 - ENSEMBL ID version conversion

Issue - State: closed - Opened by grabear about 4 years ago - 9 comments

#23 - Importing DGE data into EnrichmentBrowser

Issue - State: closed - Opened by grabearummc about 4 years ago - 14 comments
Labels: question

#23 - Importing DGE data into EnrichmentBrowser

Issue - State: closed - Opened by grabearummc about 4 years ago - 14 comments
Labels: question

#22 - Add "neat" among the nbeaMethods available in nbea

Pull Request - State: closed - Opened by mirkosignorelli over 4 years ago - 1 comment

#22 - Add "neat" among the nbeaMethods available in nbea

Pull Request - State: closed - Opened by mirkosignorelli over 4 years ago - 1 comment

#21 - Create neat.R

Pull Request - State: closed - Opened by mirkosignorelli over 4 years ago - 1 comment

#21 - Create neat.R

Pull Request - State: closed - Opened by mirkosignorelli over 4 years ago - 1 comment

#20 - Trace back ID mapping

Issue - State: closed - Opened by lgeistlinger about 5 years ago - 1 comment
Labels: enhancement

#20 - Trace back ID mapping

Issue - State: closed - Opened by lgeistlinger about 5 years ago - 1 comment
Labels: enhancement

#19 - Dead link in webinterface

Issue - State: open - Opened by bromberglab-services about 5 years ago
Labels: wontfix

#18 - eaBrowse error with S. cerevisiae org.db

Issue - State: closed - Opened by matrs over 5 years ago - 4 comments
Labels: bug

#18 - eaBrowse error with S. cerevisiae org.db

Issue - State: closed - Opened by matrs over 5 years ago - 4 comments
Labels: bug

#17 - Make Output Friendly with Shiny?

Issue - State: open - Opened by whtns over 5 years ago - 1 comment
Labels: enhancement

#17 - Make Output Friendly with Shiny?

Issue - State: open - Opened by whtns over 5 years ago - 1 comment
Labels: enhancement

#16 - Including batch effect correction

Issue - State: closed - Opened by ktmf1991 over 5 years ago - 7 comments
Labels: question

#16 - Including batch effect correction

Issue - State: closed - Opened by ktmf1991 over 5 years ago - 7 comments
Labels: question

#15 - Already have DE gene lists

Issue - State: closed - Opened by fcamus almost 6 years ago - 3 comments
Labels: question

#15 - Already have DE gene lists

Issue - State: closed - Opened by fcamus almost 6 years ago - 3 comments
Labels: question

#14 - Optionally create index page also for eaBrowse

Issue - State: closed - Opened by lgeistlinger about 6 years ago - 4 comments
Labels: enhancement

#14 - Optionally create index page also for eaBrowse

Issue - State: closed - Opened by lgeistlinger about 6 years ago - 4 comments
Labels: enhancement

#13 - error in eaBrowse when there are no significant gene sets

Issue - State: closed - Opened by olkap over 6 years ago - 2 comments
Labels: enhancement

#13 - error in eaBrowse when there are no significant gene sets

Issue - State: closed - Opened by olkap over 6 years ago - 2 comments
Labels: enhancement

#12 - error in ebrowser when a dplyr library is loaded

Issue - State: closed - Opened by olkap over 6 years ago - 2 comments
Labels: question

#12 - error in ebrowser when a dplyr library is loaded

Issue - State: closed - Opened by olkap over 6 years ago - 2 comments
Labels: question

#11 - Non-integer RNASeq data pass to deAna() when de.method = "limma"

Issue - State: closed - Opened by mctseng2 over 6 years ago - 1 comment
Labels: question

#11 - Non-integer RNASeq data pass to deAna() when de.method = "limma"

Issue - State: closed - Opened by mctseng2 over 6 years ago - 1 comment
Labels: question

#10 - Problem with creating image for hsa04215 KEGG pathway in ebrowser

Issue - State: closed - Opened by olkap over 6 years ago - 9 comments
Labels: bug

#9 - Annotation package not found using readSE

Issue - State: closed - Opened by approximately-normal over 6 years ago - 2 comments
Labels: question

#9 - Annotation package not found using readSE

Issue - State: closed - Opened by approximately-normal over 6 years ago - 2 comments
Labels: question

#8 - Request: ability to change output directory and .html file name

Issue - State: closed - Opened by jdrnevich over 6 years ago - 4 comments
Labels: enhancement

#8 - Request: ability to change output directory and .html file name

Issue - State: closed - Opened by jdrnevich over 6 years ago - 4 comments
Labels: enhancement

#7 - Error appears when using gsea in ebrowser

Issue - State: closed - Opened by olkap over 6 years ago - 5 comments
Labels: bug

#7 - Error appears when using gsea in ebrowser

Issue - State: closed - Opened by olkap over 6 years ago - 5 comments
Labels: bug

#6 - idMap/.idmap not giving the correct numbers of genes lost during conversion

Issue - State: closed - Opened by jdrnevich over 6 years ago - 8 comments
Labels: bug, enhancement

#6 - idMap/.idmap not giving the correct numbers of genes lost during conversion

Issue - State: closed - Opened by jdrnevich over 6 years ago - 8 comments
Labels: bug, enhancement

#5 - SPIA fix not correctly implemented in 2.10.3

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 2 comments
Labels: bug

#5 - SPIA fix not correctly implemented in 2.10.3

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 2 comments
Labels: bug

#4 - I'm having trouble with NetGSA

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 4 comments
Labels: bug

#4 - I'm having trouble with NetGSA

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 4 comments
Labels: bug

#3 - SPIA file connection error

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 1 comment
Labels: bug

#3 - SPIA file connection error

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 1 comment
Labels: bug

#2 - neaGUI package deprecated

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 3 comments

#2 - neaGUI package deprecated

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 3 comments

#1 - Error message when importing GO genesets

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 2 comments
Labels: question

#1 - Error message when importing GO genesets

Issue - State: closed - Opened by Ju-Rien over 6 years ago - 2 comments
Labels: question

GitHub / lgeistlinger/enrichmentbrowser issues and pull requests