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
#84 - Ensure heatmap bin legend is ordered in the same way as the heatmap columns
Pull Request -
State: closed - Opened by csoneson 16 days ago
#83 - Make sure that the heatmap bin legend is ordered in the same way as the columns of the heatmaps
Issue -
State: closed - Opened by csoneson 17 days ago
#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
#77 - not reproducible results - set.seed is not considered by calcBinnedMotifEnrR
Issue -
State: closed - Opened by NathanHarmston 8 months ago
- 2 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