neurogenomics/EpiCompare

Issues

• push to Bioconductor RELEASE_3_17

  #150 opened 4 months ago by serachoi1230
  2

• GHA Windows: `Parser error: while parsing a block mapping at line 1, column 1 did not find expected key at line 1, column 45`

  #146 opened a year ago by bschilder
  6

• EpiCompare failing on Bioc Windows

  #153 opened 2 years ago by bschilder
  15

• EpiCompare Function Error - Unable to find an inherited method for function 'mcols'

  #152 opened 2 years ago by ParisaRahbar
  1

• GHA Linux: `Error in grid.newpage(): could not open file `

  #147 opened 2 years ago by bschilder
  6

• `WARNING: The following files are over 5MB in size: 'inst/doc/example_report.html'`

  #151 opened 2 years ago by bschilder
  3

• Options to display plots side-by-side

  #134 opened 2 years ago by bschilder
  1

• `EpiCompare::EpiCompare`: Automatically choose blacklist

  #113 opened 2 years ago by bschilder
  1

• Issues with download button

  #148 opened 2 years ago by serachoi1230
  12

• Add chromatin mark data to example report

  #124 opened 2 years ago by bschilder
  3

• Update NEWS file

  #149 opened 2 years ago by bschilder
  0

• User-specified TSS-distance

  #131 opened 2 years ago by bschilder
  1

• `Error: processing vignette 'EpiCompare.Rmd' failed with diagnostics: [ENOENT] Failed to remove `

  #138 opened 2 years ago by bschilder
  8

• Percentage overlap: bar plot

  #128 opened 2 years ago by bschilder
  3

• Supply message indicating which feature were NOT run

  #145 opened 2 years ago by bschilder
  1

• Add debug mode

  #144 opened 2 years ago by bschilder
  1

• Reduce dependencies

  #143 opened 2 years ago by bschilder
  0

• `downloadthis:::download_this.ggplot(...)`: `Error: ! Unknown graphics device "rds"`

  #142 opened 2 years ago by bschilder
  2

• Add citation information

  #141 opened 2 years ago by bschilder
  0

• Make custom EpiCompare Rmarkdown theme

  #140 opened 2 years ago by bschilder
  0

• Report `EpiCompare` command

  #139 opened 2 years ago by bschilder
  0

• Pull Bioc `RELEASE_3_16`

  #122 opened 2 years ago by bschilder
  12

• Save "uplifted" peak/bed files

  #135 opened 2 years ago by bschilder
  2

• Could you add T2Tv2.0 new assembly (so called Hs1) to hg19 and hg38? Thanks

  #137 opened 2 years ago by josegarciamanteiga
  3

• Add note about documentation/Bioc version differences

  #136 opened 2 years ago by bschilder
  1

• New options for ChromHMM annotations or an option for the user to choose their own annotation

  #119 opened 2 years ago by teemuronkko
  1

• list all blacklist options

  #130 opened 2 years ago by bschilder
  0

• Label TSS plots

  #132 opened 2 years ago by bschilder
  0

• Add mouse blacklists

  #129 opened 2 years ago by bschilder
  0

• `general metrics: peak reports`: auto-rescale

  #125 opened 2 years ago by bschilder
  0

• percentage overlap plots: improvements

  #126 opened 2 years ago by bschilder
  1

• Add more informative Suggest dep messages

  #133 opened 2 years ago by bschilder
  1

• `EpiCompare::EpiCompare`: Consider add `run_all` arg

  #127 opened 2 years ago by bschilder
  2

• GHA Windows: ` there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'`

  #117 opened 2 years ago by bschilder
  1

• Bioconductor checks failing on Linux:

  #121 opened 2 years ago by bschilder
  1

• Add rworkflows

  #123 opened 2 years ago by bschilder
  0

• Add consensus motif detection to EpiCompare so we can better analyse transcription factor data

  #114 opened 2 years ago by NathanSkene
  0

• Get Picard summary metrics from <batch>/02_alignment/bowtie2/target/sample_name.stats file

  #118 opened 2 years ago by teemuronkko
  5

• Save precision-recall and correlation results

  #120 opened 2 years ago by bschilder
  1

• Submit `EpiCompare` manuscript to peer-reviewed journal

  #109 opened 2 years ago by bschilder
  0

• Cannot push to Bioconductor

  #115 opened 2 years ago by serachoi1230
  3

• Functional Enrichment Analysis: generate separate plots for each peak set

  #116 opened 2 years ago by bschilder
  0

• EpiCompare report replacing Get started vignette

  #112 opened 2 years ago by bschilder
  1

• Reduce size of *EpiCompare_example.html*

  #106 opened 2 years ago by bschilder
  1

• unused argument

  #111 opened 2 years ago by Kebabai9
  1

• Unable to find chain files on `AnnotationHub`

  #105 opened 2 years ago by bschilder
  1

• Update CITATION file

  #110 opened 2 years ago by bschilder
  0

• Submit`EpiCompare` manuscript to bioRxiv

  #108 opened 2 years ago by bschilder
  0

• Update README

  #107 opened 2 years ago by bschilder
  0

• Plot peaks across chromosomes

  #104 opened 2 years ago by bschilder
  0