neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

https://doi.org/doi:10.18129/B9.bioc.EpiCompare

neurogenomics/EpiCompare Issues

GHA Windows: `Parser error: while parsing a block mapping at line 1, column 1 did not find expected key at line 1, column 45`
Closed 6 months ago6
EpiCompare failing on Bioc Windows
Updated 9 months ago15
EpiCompare Function Error - Unable to find an inherited method for function 'mcols'
Updated a year ago1
GHA Linux: `Error in grid.newpage(): could not open file `
Closed a year ago6
`WARNING: The following files are over 5MB in size: 'inst/doc/example_report.html'`
Closed a year ago3
Options to display plots side-by-side
Closed a year ago1
push to Bioconductor RELEASE_3_17
Updated a year ago2
`EpiCompare::EpiCompare`: Automatically choose blacklist
Closed a year ago1
Issues with download button
Updated a year ago12
Add chromatin mark data to example report
Closed a year ago3
Update NEWS file
Updated a year ago
User-specified TSS-distance
Closed a year ago1
`Error: processing vignette 'EpiCompare.Rmd' failed with diagnostics: [ENOENT] Failed to remove `
Closed a year ago8
Percentage overlap: bar plot
Closed a year ago3
Supply message indicating which feature were NOT run
Closed a year ago1
Add debug mode
Closed a year ago1
Reduce dependencies
Updated a year ago
`downloadthis:::download_this.ggplot(...)`: `Error: ! Unknown graphics device "rds"`
Closed a year ago2
Add citation information
Closed a year ago
Make custom EpiCompare Rmarkdown theme
Closed a year ago
Report `EpiCompare` command
Closed a year ago
Pull Bioc `RELEASE_3_16`
Closed a year ago12
Save "uplifted" peak/bed files
Closed a year ago2
Could you add T2Tv2.0 new assembly (so called Hs1) to hg19 and hg38? Thanks
Updated a year ago3
Add note about documentation/Bioc version differences
Closed a year ago1
New options for ChromHMM annotations or an option for the user to choose their own annotation
Updated a year ago1
list all blacklist options
Closed a year ago
Label TSS plots
Closed a year ago
Add mouse blacklists
Closed a year ago
`general metrics: peak reports`: auto-rescale
Closed a year ago
percentage overlap plots: improvements
Closed a year ago1
Add more informative Suggest dep messages
Closed a year ago1
`EpiCompare::EpiCompare`: Consider add `run_all` arg
Closed a year ago2
GHA Windows: ` there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'`
Closed 2 years ago1
Bioconductor checks failing on Linux:
Closed 2 years ago1
Add rworkflows
Closed 2 years ago
Add consensus motif detection to EpiCompare so we can better analyse transcription factor data
Updated 2 years ago
Get Picard summary metrics from <batch>/02_alignment/bowtie2/target/sample_name.stats file
Closed 2 years ago5
Save precision-recall and correlation results
Closed 2 years ago1
Submit `EpiCompare` manuscript to peer-reviewed journal
Closed 2 years ago
Cannot push to Bioconductor
Closed 2 years ago3
Functional Enrichment Analysis: generate separate plots for each peak set
Updated 2 years ago
EpiCompare report replacing Get started vignette
Closed 2 years ago1
Reduce size of *EpiCompare_example.html*
Closed 2 years ago1
unused argument
Closed 2 years ago1
Unable to find chain files on `AnnotationHub`
Closed 2 years ago1
Update CITATION file
Closed 2 years ago
Submit`EpiCompare` manuscript to bioRxiv
Closed 2 years ago
Update README
Closed 2 years ago
Plot peaks across chromosomes
Updated 2 years ago