Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / fmicompbio/monaLisa issues and pull requests

#82 - Switch to ggplot2 for violin plots?

Issue - State: open - Opened by csoneson 20 days ago

#81 - Update cache action

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

#80 - Update upload-artifact action

Pull Request - State: closed - Opened by csoneson 4 months ago

#79 - issue #62, add legend with bin labels to plotMotifHeatmaps

Pull Request - State: closed - Opened by danymukesha 4 months ago - 4 comments

#78 - Problem of plotMotifHeatmaps function - missing motif logos

Issue - State: closed - Opened by leezx 7 months ago - 4 comments

#76 - Update actions

Pull Request - State: closed - Opened by csoneson 9 months ago

#75 - Heatmap logo annotation broken using grid.grabExpr()

Issue - State: closed - Opened by IStevant 9 months ago - 2 comments

#74 - using motifs from both JASPAR and homer

Issue - State: closed - Opened by cxtaslim 10 months ago - 3 comments

#73 - omnibus test for binned approach

Issue - State: open - Opened by machlabd 10 months ago
Labels: enhancement

#72 - binned enrichment analysis for sets of motifs

Issue - State: open - Opened by mbstadler 10 months ago
Labels: enhancement

#71 - Adapt to new JASPAR

Pull Request - State: closed - Opened by mbstadler 10 months ago - 2 comments

#70 - how to plot motifs with negative enrichment

Issue - State: closed - Opened by cxtaslim 10 months ago - 5 comments

#69 - genome background never finished

Issue - State: closed - Opened by olechnwin 10 months ago - 3 comments

#68 - Issue with JASPAR2024

Issue - State: closed - Opened by nsoriano2 10 months ago - 4 comments

#67 - Error - bin() - .... 'breaks' are not unique

Issue - State: closed - Opened by matteozoia4 over 1 year ago - 2 comments

#66 - The nature of the Markov models

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

#65 - dumpJaspar function

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

#64 - Motif name size

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

#63 - how to set the text size of the motif names in plotMotifHeatmaps function?

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

#62 - Add legend with bin labels to heatmap

Issue - State: closed - Opened by csoneson about 2 years ago - 3 comments
Labels: enhancement

#61 - Return genomic coordinates of sampled background set

Issue - State: open - Opened by csoneson about 2 years ago
Labels: enhancement

#60 - `show_seqlogo` option does not work in `plotMotifHeatmaps` function

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

#59 - Use Bioc actions, change to devel

Pull Request - State: closed - Opened by csoneson over 2 years ago - 7 comments

#58 - Fix seqlogo

Pull Request - State: closed - Opened by csoneson almost 3 years ago

#57 - Add bioinf citation

Pull Request - State: closed - Opened by machlabd almost 3 years ago - 2 comments

#56 - Impact of highly correlated motifs on the binned approach

Issue - State: closed - Opened by lengfei5 almost 3 years ago - 5 comments

#55 - results from enrichment analysis differs each run

Issue - State: closed - Opened by zhezhenwang almost 3 years ago - 4 comments

#54 - Updates to monaLisa for revision

Pull Request - State: closed - Opened by mbstadler about 3 years ago - 1 comment

#53 - use R devel on GHA

Pull Request - State: closed - Opened by mbstadler over 3 years ago

#52 - Fix monalisa-package.R file

Pull Request - State: closed - Opened by machlabd over 3 years ago

#51 - Suppress warnings from matchPWM in regression vignette

Pull Request - State: closed - Opened by csoneson over 3 years ago - 1 comment

#50 - Update logo in read me

Pull Request - State: closed - Opened by machlabd over 3 years ago - 1 comment

#49 - Fix regression vignette

Pull Request - State: closed - Opened by csoneson over 3 years ago - 1 comment

#48 - Minor fixes

Pull Request - State: closed - Opened by mbstadler over 3 years ago

#47 - Kmers to motifs

Pull Request - State: closed - Opened by mbstadler over 3 years ago - 1 comment

#46 - sort functions for BioC submission

Issue - State: closed - Opened by mbstadler over 3 years ago - 1 comment

#45 - Various fixes

Pull Request - State: closed - Opened by csoneson over 3 years ago - 2 comments

#44 - Adaptations to simplify making kmer/motif plots

Pull Request - State: closed - Opened by csoneson over 3 years ago - 2 comments

#43 - Fix pearson resid

Pull Request - State: closed - Opened by mbstadler over 3 years ago - 1 comment

#42 - Rand lasso deterministic

Pull Request - State: closed - Opened by machlabd over 3 years ago - 1 comment

#41 - Fix breaks equal width

Pull Request - State: closed - Opened by mbstadler over 3 years ago - 1 comment

#40 - More to do fixes

Pull Request - State: closed - Opened by machlabd over 3 years ago - 1 comment

#39 - More params

Pull Request - State: closed - Opened by mbstadler almost 4 years ago

#38 - A few typos

Pull Request - State: closed - Opened by csoneson almost 4 years ago

#37 - Homers better looking twin

Pull Request - State: closed - Opened by mbstadler almost 4 years ago - 1 comment

#36 - get ready for submission to Bioconductor

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

#35 - Add options for binned motif enrichment

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

#34 - count k-mer pairs

Pull Request - State: closed - Opened by mbstadler almost 5 years ago - 1 comment

#33 - Cluster kmers

Pull Request - State: closed - Opened by mbstadler about 5 years ago - 1 comment

#32 - add option to `kmerEnrichments` to define background

Issue - State: closed - Opened by mbstadler about 5 years ago - 2 comments

#31 - Add stabsel directionality plot 2

Pull Request - State: closed - Opened by machlabd about 5 years ago - 3 comments

#30 - cluster (enriched) k-mers

Issue - State: closed - Opened by mbstadler about 5 years ago - 2 comments

#29 - create artificial dataset

Issue - State: closed - Opened by mbstadler about 5 years ago - 1 comment

#28 - not depend on HOMER

Issue - State: closed - Opened by mbstadler about 5 years ago - 4 comments

#27 - make getKmerFreq accept a Granges object

Issue - State: closed - Opened by machlabd about 5 years ago - 1 comment

#26 - Add plot for stabsel

Pull Request - State: closed - Opened by machlabd about 5 years ago - 1 comment

#25 - Check homer run

Pull Request - State: closed - Opened by machlabd over 5 years ago - 1 comment

#24 - return count matrix from HOMER run

Issue - State: closed - Opened by LukasBurger over 5 years ago - 1 comment

#23 - `motifSimilarity` (former `clusterPWMs`) features

Issue - State: open - Opened by mbstadler over 5 years ago - 2 comments

#22 - centralised, consistent definition of HOMER installation

Issue - State: closed - Opened by mbstadler over 5 years ago - 2 comments

#21 - Summarized experiment

Pull Request - State: closed - Opened by mbstadler over 5 years ago

#20 - make runHomer check whether output files already exist

Issue - State: closed - Opened by LukasBurger over 5 years ago - 4 comments

#19 - make function that takes homer motif file and converts to PWM object

Issue - State: closed - Opened by machlabd over 5 years ago - 1 comment

#18 - add PWM logos to heatmap

Issue - State: closed - Opened by LukasBurger over 5 years ago - 2 comments

#17 - add citation of Pauls and Darkos paper

Issue - State: closed - Opened by LukasBurger over 5 years ago - 1 comment

#16 - add GC content of PWMs column to heatmap and summarised experiment

Issue - State: closed - Opened by LukasBurger over 5 years ago - 1 comment

#15 - change naming of PWMs

Issue - State: closed - Opened by LukasBurger over 5 years ago - 2 comments

#14 - make comment on problem if regions are of different length

Issue - State: closed - Opened by LukasBurger over 5 years ago - 2 comments

#13 - summarized experiment for enrichment/pvalue etc

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

#12 - Lisa on motifs from de novo motif finding?

Issue - State: open - Opened by LukasBurger over 5 years ago - 1 comment

#9 - option to plot enrichment heat map without motifs enriched in central bin

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

#8 - clustering of motifs

Issue - State: closed - Opened by LukasBurger over 5 years ago - 2 comments

#7 - legend font size in plotBinScatter

Issue - State: closed - Opened by LukasBurger over 5 years ago - 2 comments

#6 - seqLogo function dependency

Issue - State: closed - Opened by LukasBurger over 5 years ago - 1 comment

#5 - Stab sel

Pull Request - State: closed - Opened by machlabd almost 6 years ago - 9 comments

#4 - maximal sequence length for homer2

Issue - State: closed - Opened by mbstadler almost 6 years ago - 1 comment

#2 - log-odds score cutoff when dumping PWMs to a file

Issue - State: open - Opened by mbstadler almost 7 years ago - 1 comment

#1 - Ideas

Issue - State: closed - Opened by LukasBurger almost 7 years ago - 4 comments