fmicompbio/monaLisa

Issues

• Make sure that the heatmap bin legend is ordered in the same way as the columns of the heatmaps

  #83 opened 2 months ago by csoneson
  0

• Switch to ggplot2 for violin plots?

  #82 opened 3 months ago by csoneson
  0

• Add legend with bin labels to heatmap

  #62 opened 6 months ago by csoneson
  3

• Problem of plotMotifHeatmaps function - missing motif logos

  #78 opened 8 months ago by leezx
  4

• not reproducible results - set.seed is not considered by calcBinnedMotifEnrR

  #77 opened 9 months ago by NathanHarmston
  2

• Heatmap logo annotation broken using grid.grabExpr()

  #75 opened a year ago by IStevant
  2

• using motifs from both JASPAR and homer

  #74 opened a year ago by cxtaslim
  3

• Issue with JASPAR2024

  #68 opened a year ago by nsoriano2
  4

• how to plot motifs with negative enrichment

  #70 opened a year ago by cxtaslim
  5

• omnibus test for binned approach

  #73 opened a year ago by machlabd
  0

• binned enrichment analysis for sets of motifs

  #72 opened a year ago by mbstadler
  0

• genome background never finished

  #69 opened a year ago by olechnwin
  3

• Error - bin() - .... 'breaks' are not unique

  #67 opened 2 years ago by matteozoia4
  2

• dumpJaspar function

  #65 opened 2 years ago by Smartmandm
  3

• how to set the text size of the motif names in plotMotifHeatmaps function?

  #63 opened 2 years ago by xflicsu
  2

• The nature of the Markov models

  #66 opened 2 years ago by stianale
  1

• Return genomic coordinates of sampled background set

  #61 opened 2 years ago by csoneson
  0

• `show_seqlogo` option does not work in `plotMotifHeatmaps` function

  #60 opened 3 years ago by jmodlis
  4

• results from enrichment analysis differs each run

  #55 opened 3 years ago by zhezhenwang
  4

• Impact of highly correlated motifs on the binned approach

  #56 opened 3 years ago by lengfei5
  5

• get ready for submission to Bioconductor

  #36 opened 3 years ago by mbstadler
  2

• sort functions for BioC submission

  #46 opened 3 years ago by mbstadler
  1

• make comment on problem if regions are of different length

  #14 opened 4 years ago by LukasBurger
  2

• create artificial dataset

  #29 opened 4 years ago by mbstadler
  1

• return count matrix from HOMER run

  #24 opened 4 years ago by LukasBurger
  1

• option to plot enrichment heat map without motifs enriched in central bin

  #9 opened 4 years ago by LukasBurger
  3

• `motifSimilarity` (former `clusterPWMs`) features

  #23 opened 6 years ago by mbstadler
  2

• not depend on HOMER

  #28 opened 4 years ago by mbstadler
  4

• Add options for binned motif enrichment

  #35 opened 4 years ago by machlabd
  2

• log-odds score cutoff when dumping PWMs to a file

  #2 opened 7 years ago by mbstadler
  1

• centralised, consistent definition of HOMER installation

  #22 opened 4 years ago by mbstadler
  2

• make getKmerFreq accept a Granges object

  #27 opened 4 years ago by machlabd
  1

• cluster (enriched) k-mers

  #30 opened 5 years ago by mbstadler
  2

• add option to `kmerEnrichments` to define background

  #32 opened 5 years ago by mbstadler
  2

• make runHomer check whether output files already exist

  #20 opened 5 years ago by LukasBurger
  4

• add citation of Pauls and Darkos paper

  #17 opened 6 years ago by LukasBurger
  1

• maximal sequence length for homer2

  #4 opened 6 years ago by mbstadler
  1

• add PWM logos to heatmap

  #18 opened 6 years ago by LukasBurger
  2

• change naming of PWMs

  #15 opened 6 years ago by LukasBurger
  2

• add GC content of PWMs column to heatmap and summarised experiment

  #16 opened 6 years ago by LukasBurger
  1

• make function that takes homer motif file and converts to PWM object

  #19 opened 6 years ago by machlabd
  1

• summarized experiment for enrichment/pvalue etc

  #13 opened 6 years ago by LukasBurger
  3

• Ideas

  #1 opened 6 years ago by LukasBurger
  4

• seqLogo function dependency

  #6 opened 6 years ago by LukasBurger
  1

• legend font size in plotBinScatter

  #7 opened 6 years ago by LukasBurger
  2

• Lisa on motifs from de novo motif finding?

  #12 opened 6 years ago by LukasBurger
  1

• clustering of motifs

  #8 opened 6 years ago by LukasBurger
  2