Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / neurogenomics/epicompare issues and pull requests
#153 - EpiCompare failing on Bioc Windows
Issue -
State: open - Opened by bschilder about 1 year ago
- 15 comments
Labels: bug
#152 - EpiCompare Function Error - Unable to find an inherited method for function 'mcols'
Issue -
State: open - Opened by ParisaRahbar about 1 year ago
- 1 comment
Labels: bug
#151 - `WARNING: The following files are over 5MB in size: 'inst/doc/example_report.html'`
Issue -
State: closed - Opened by bschilder over 1 year ago
- 3 comments
Labels: bug, GitHub Actions
#150 - push to Bioconductor RELEASE_3_17
Issue -
State: open - Opened by serachoi1230 over 1 year ago
- 2 comments
#149 - Update NEWS file
Issue -
State: open - Opened by bschilder over 1 year ago
Labels: documentation
#148 - Issues with download button
Issue -
State: open - Opened by serachoi1230 over 1 year ago
- 12 comments
Labels: bug
#147 - GHA Linux: `Error in grid.newpage(): could not open file `
Issue -
State: closed - Opened by bschilder over 1 year ago
- 6 comments
Labels: bug, help wanted, GitHub Actions
#146 - GHA Windows: `Parser error: while parsing a block mapping at line 1, column 1 did not find expected key at line 1, column 45`
Issue -
State: closed - Opened by bschilder over 1 year ago
- 6 comments
Labels: bug, help wanted, GitHub Actions
#145 - Supply message indicating which feature were NOT run
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: documentation, enhancement
#144 - Add debug mode
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: enhancement
#143 - Reduce dependencies
Issue -
State: open - Opened by bschilder over 1 year ago
Labels: enhancement
#142 - `downloadthis:::download_this.ggplot(...)`: `Error: ! Unknown graphics device "rds"`
Issue -
State: closed - Opened by bschilder over 1 year ago
- 2 comments
Labels: bug
#141 - Add citation information
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: documentation, enhancement
#140 - Make custom EpiCompare Rmarkdown theme
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: enhancement
#139 - Report `EpiCompare` command
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: enhancement
#138 - `Error: processing vignette 'EpiCompare.Rmd' failed with diagnostics: [ENOENT] Failed to remove `
Issue -
State: closed - Opened by bschilder over 1 year ago
- 8 comments
Labels: bug, help wanted
#137 - Could you add T2Tv2.0 new assembly (so called Hs1) to hg19 and hg38? Thanks
Issue -
State: open - Opened by josegarciamanteiga over 1 year ago
- 3 comments
Labels: enhancement
#136 - Add note about documentation/Bioc version differences
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: documentation
#135 - Save "uplifted" peak/bed files
Issue -
State: closed - Opened by bschilder over 1 year ago
- 2 comments
Labels: enhancement
#134 - Options to display plots side-by-side
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: enhancement
#133 - Add more informative Suggest dep messages
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: documentation, enhancement
#132 - Label TSS plots
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: documentation, enhancement
#131 - User-specified TSS-distance
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: enhancement
#130 - list all blacklist options
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: documentation
#129 - Add mouse blacklists
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: enhancement
#128 - Percentage overlap: bar plot
Issue -
State: closed - Opened by bschilder over 1 year ago
- 3 comments
Labels: enhancement
#127 - `EpiCompare::EpiCompare`: Consider add `run_all` arg
Issue -
State: closed - Opened by bschilder over 1 year ago
- 2 comments
Labels: enhancement
#126 - percentage overlap plots: improvements
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: enhancement
#125 - `general metrics: peak reports`: auto-rescale
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: enhancement
#124 - Add chromatin mark data to example report
Issue -
State: closed - Opened by bschilder over 1 year ago
- 3 comments
Labels: documentation, enhancement
#123 - Add rworkflows
Issue -
State: closed - Opened by bschilder over 1 year ago
Labels: GitHub Actions
#122 - Pull Bioc `RELEASE_3_16`
Issue -
State: closed - Opened by bschilder over 1 year ago
- 12 comments
Labels: documentation
#121 - Bioconductor checks failing on Linux:
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: bug
#120 - Save precision-recall and correlation results
Issue -
State: closed - Opened by bschilder over 1 year ago
- 1 comment
Labels: enhancement
#119 - New options for ChromHMM annotations or an option for the user to choose their own annotation
Issue -
State: open - Opened by teemuronkko almost 2 years ago
- 1 comment
Labels: enhancement
#118 - Get Picard summary metrics from <batch>/02_alignment/bowtie2/target/sample_name.stats file
Issue -
State: closed - Opened by teemuronkko almost 2 years ago
- 5 comments
Labels: bug
#117 - GHA Windows: ` there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'`
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 1 comment
Labels: GitHub Actions
#116 - Functional Enrichment Analysis: generate separate plots for each peak set
Issue -
State: open - Opened by bschilder almost 2 years ago
Labels: enhancement
#115 - Cannot push to Bioconductor
Issue -
State: closed - Opened by serachoi1230 almost 2 years ago
- 3 comments
Labels: bug
#114 - Add consensus motif detection to EpiCompare so we can better analyse transcription factor data
Issue -
State: open - Opened by NathanSkene almost 2 years ago
Labels: enhancement
#113 - `EpiCompare::EpiCompare`: Automatically choose blacklist
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 1 comment
Labels: enhancement
#112 - EpiCompare report replacing Get started vignette
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 1 comment
Labels: documentation
#111 - unused argument
Issue -
State: closed - Opened by Kebabai9 almost 2 years ago
- 1 comment
Labels: bug
#110 - Update CITATION file
Issue -
State: closed - Opened by bschilder almost 2 years ago
#109 - Submit `EpiCompare` manuscript to peer-reviewed journal
Issue -
State: closed - Opened by bschilder almost 2 years ago
Labels: enhancement
#108 - Submit`EpiCompare` manuscript to bioRxiv
Issue -
State: closed - Opened by bschilder almost 2 years ago
#107 - Update README
Issue -
State: closed - Opened by bschilder almost 2 years ago
#106 - Reduce size of *EpiCompare_example.html*
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 1 comment
#105 - Unable to find chain files on `AnnotationHub`
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 1 comment
Labels: bug
#104 - Plot peaks across chromosomes
Issue -
State: open - Opened by bschilder almost 2 years ago
Labels: enhancement
#103 - `rebin_peaks`: `Error in data.table::rbindlist(rebinned_peaks, use.names = TRUE, idcol = "assay") :
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 5 comments
Labels: bug
#102 - Function overlap_percent report error unused arguments (peaklist1 = peaks, peaklist2 = reference_peak)
Issue -
State: closed - Opened by Xindong-Sun almost 2 years ago
- 2 comments
Labels: bug
#101 - Make `rebin_peaks` more efficient
Issue -
State: closed - Opened by bschilder almost 2 years ago
- 1 comment
Labels: enhancement
#100 - Error report when running the EpiCompare (github version, 0.99.21) with precision and recall curve
Issue -
State: closed - Opened by Xindong-Sun about 2 years ago
- 1 comment
Labels: bug
#99 - Advertise docker container
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: documentation
#98 - Address limitations of consensus peak calling
Issue -
State: open - Opened by bschilder about 2 years ago
Labels: enhancement
#97 - Return paths to html files
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: enhancement
#96 - Fix file paths when reference >1
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: bug
#95 - Low precision-recall in example
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
Labels: bug
#94 - `compute_corr()`: Benchmark how bin sizes affect correlations
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
Labels: enhancement
#93 - Create consensus peaks
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
Labels: enhancement
#92 - Liftover causes extra weird chromosomes
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
Labels: bug
#91 - Check overlap_percent()
Issue -
State: closed - Opened by serachoi1230 about 2 years ago
#90 - Collapse code instead of removing entirely
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
Labels: enhancement
#89 - Enable mapping to/from mm9
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: enhancement
#88 - `Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), : duplicate row.names: all`
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
Labels: bug
#87 - Bioc checks
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
Labels: bug
#86 - Open report after done generating
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: enhancement
#85 - Capture peak input URLs
Issue -
State: open - Opened by bschilder about 2 years ago
Labels: enhancement
#84 - Add hex logo
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
#83 - Enable filtering of peaks
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
Labels: enhancement
#82 - `overlap_percent`: Handle `length(peaklist2)>1`
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
#81 - Add x/y axis label wrapping
Issue -
State: open - Opened by bschilder about 2 years ago
Labels: enhancement
#80 - Add precision/recall plots
Issue -
State: closed - Opened by bschilder about 2 years ago
- 5 comments
Labels: enhancement
#79 - `gather_files`: Annotate headers
Issue -
State: closed - Opened by bschilder about 2 years ago
#78 - Required/ Suggested imports
Issue -
State: closed - Opened by serachoi1230 about 2 years ago
- 1 comment
#77 - Save plot data
Issue -
State: closed - Opened by bschilder about 2 years ago
- 3 comments
Labels: enhancement
#76 - `EpiCompare::EpiCompare`: return output file path(s)
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: enhancement
#75 - Standardise genome builds
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
#74 - `plot_chromHMM`: sort X-axis
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: enhancement
#73 - Add timer to `EpiCompare::EpiCompare`
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: enhancement
#72 - Improve `EpiCompare` efficiency
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
Labels: enhancement
#71 - Handle `reference` with length >1
Issue -
State: closed - Opened by bschilder about 2 years ago
- 3 comments
#70 - Document genome builds of each built-in dataset
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: documentation
#69 - Shorten code by setting names while making list
Issue -
State: closed - Opened by bschilder about 2 years ago
#68 - Use "\code{}" instead of "``" in Roxygen notes
Issue -
State: closed - Opened by bschilder about 2 years ago
Labels: documentation
#67 - Simplify loops
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
Labels: enhancement
#66 - Remove `S4Vectors` dep
Issue -
State: closed - Opened by bschilder about 2 years ago
#65 - Replace write.table with fwrite
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
#64 - Make dedicated liftover function
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
#63 - Run `plot_chromHMM` example
Issue -
State: closed - Opened by bschilder about 2 years ago
- 2 comments
#62 - Require `TxDb.Hsapiens.UCSC.**.knownGene`
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
#61 - Use multiple genome builds
Issue -
State: closed - Opened by bschilder about 2 years ago
- 10 comments
#60 - Explain what the picard summary file is
Issue -
State: closed - Opened by NathanSkene about 2 years ago
Labels: documentation
#59 - `error in evaluating the argument 'x' in selecting a method for function 'elementMetadata': GRanges objects don't support [[`
Issue -
State: closed - Opened by bschilder about 2 years ago
- 8 comments
#58 - `import_narrowPeak`
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
#57 - Fix GHA
Issue -
State: closed - Opened by bschilder about 2 years ago
- 1 comment
#43 - Include API to ENCODE data
Issue -
State: closed - Opened by bschilder over 2 years ago
- 4 comments
Labels: enhancement
#41 - Add codecov badge
Issue -
State: closed - Opened by bschilder over 2 years ago
- 2 comments
#40 - Create function-specific unit tests
Issue -
State: open - Opened by bschilder over 2 years ago
- 1 comment
Labels: documentation, enhancement