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

#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

#101 - Make `rebin_peaks` more efficient

Issue - State: closed - Opened by bschilder almost 2 years ago - 1 comment
Labels: enhancement

#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

#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

#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