Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / phanstiellab/plotgardener issues and pull requests

#133 - Cool file BALANCE normalization

Issue - State: open - Opened by claricehong 6 months ago - 1 comment

#132 - Fixing the range scale in plotMultiSignal() function

Issue - State: open - Opened by Delta-43 7 months ago
Labels: bug

#131 - Updating maintainers (devel)

Pull Request - State: closed - Opened by nekramer 7 months ago

#130 - Updating maintainers (devel)

Pull Request - State: closed - Opened by nekramer 7 months ago

#129 - Update maintainers

Pull Request - State: closed - Opened by nekramer 7 months ago

#128 - attempt to add a tx filter

Pull Request - State: open - Opened by mikelove 7 months ago - 1 comment

#127 - plotPairs

Pull Request - State: closed - Opened by aberhanu 7 months ago

#126 - Cool files

Pull Request - State: closed - Opened by nekramer 8 months ago - 1 comment

#125 - Option to make a plottranscript()

Issue - State: open - Opened by seyoun209 8 months ago - 1 comment

#124 - Plottranscripts patch

Pull Request - State: closed - Opened by nekramer 8 months ago

#123 - plotTranscripts bug fix issue #122

Pull Request - State: closed - Opened by nekramer 8 months ago

#122 - Bug in plotTranscripts() labels argument

Issue - State: closed - Opened by JiayuSuPKU 8 months ago - 1 comment

#121 - Nekramer pairs checking

Pull Request - State: closed - Opened by nekramer 8 months ago

#120 - pairs anchor order checking and swapping re issue #116

Pull Request - State: closed - Opened by nekramer 8 months ago

#119 - Update issue templates

Pull Request - State: closed - Opened by nekramer 8 months ago

#118 - Pagecreate patch

Pull Request - State: closed - Opened by nekramer 8 months ago

#117 - Pagecreate patch

Pull Request - State: closed - Opened by nekramer 8 months ago

#116 - plotpairsarches error

Issue - State: closed - Opened by TamDunlop 8 months ago - 14 comments

#115 - Cannot specify location using plotHicTriangle

Issue - State: closed - Opened by Ziwei-Liu 9 months ago - 2 comments

#114 - generate TxDb for non-model organism

Issue - State: closed - Opened by sadikmz 10 months ago - 3 comments

#113 - Hicsquare rot

Pull Request - State: closed - Opened by nekramer 10 months ago

#112 - plotHicSquare rotate by 90 degrees

Issue - State: closed - Opened by khayer 10 months ago - 3 comments

#111 - plotManhattan GRanges bug fix merged from RELEASE

Pull Request - State: closed - Opened by nekramer 10 months ago

#110 - plotManhattan GRanges bug fix

Pull Request - State: closed - Opened by nekramer 10 months ago - 1 comment

#109 - Annotate multiple SNPs with rsID on a Manhattan plot

Issue - State: open - Opened by Knetsy 10 months ago - 2 comments

#108 - annoYaxis sizing Correct for one plot but incorrect for other 3 plots

Issue - State: closed - Opened by dlabuz 10 months ago - 2 comments

#107 - plotManhattan says `data` can be `GRanges`

Issue - State: closed - Opened by mikelove 11 months ago

#106 - Using tibble for geneHighlights

Issue - State: closed - Opened by maxim-h about 1 year ago - 2 comments
Labels: bug

#105 - Feature request: placing ggplot components separately

Issue - State: open - Opened by pieterjanvc about 1 year ago - 2 comments
Labels: enhancement

#104 - Update plotIdeogram documentation to include `flip`

Pull Request - State: closed - Opened by sarmapar about 1 year ago - 1 comment

#103 - Adding flip parameter to plotIdeogram

Pull Request - State: closed - Opened by sarmapar about 1 year ago - 1 comment
Labels: enhancement, in progress

#102 - Flipping chromosome start/end in plotIdeogram

Issue - State: closed - Opened by sarmapar about 1 year ago - 1 comment
Labels: enhancement, in progress

#101 - Plotgenes() and plottranscript () error in hg38

Issue - State: closed - Opened by seyoun209 over 1 year ago - 1 comment

#100 - add SNP and related text to the figure

Issue - State: closed - Opened by linpei26 over 1 year ago - 2 comments

#98 - multiple PVALB genes/plotting PVALB in wrong location?

Issue - State: closed - Opened by nekramer over 1 year ago
Labels: bug

#97 - `readHic` no data found

Issue - State: open - Opened by nekramer over 1 year ago - 3 comments

#96 - Support for labeling multiple genes that are close together

Issue - State: open - Opened by sup27606 over 1 year ago - 1 comment
Labels: enhancement

#95 - plotPairsArches, archHeight, Y-axis

Issue - State: open - Opened by Elliott77 over 1 year ago - 4 comments

#94 - Pdflen testing

Pull Request - State: closed - Opened by nekramer over 1 year ago

#93 - PlotTranscripts not annotating all the transcripts of a given gene

Issue - State: open - Opened by NPSDC over 1 year ago - 5 comments
Labels: enhancement

#92 - flip plot from plotSignal

Issue - State: closed - Opened by RobTesf over 1 year ago - 3 comments

#91 - annoYaxis makes a new page when writing to PDF when axisLine = FALSE

Issue - State: closed - Opened by ksmetz over 1 year ago - 1 comment

#90 - Blankpage patch

Pull Request - State: closed - Opened by nekramer over 1 year ago

#89 - Blankpage patch

Pull Request - State: closed - Opened by nekramer over 1 year ago

#88 - readHiC observed counts calculation

Issue - State: closed - Opened by chualec over 1 year ago - 2 comments

#86 - Fixes #85

Pull Request - State: closed - Opened by EricSDavis over 1 year ago - 1 comment

#85 - Blank page on pdf()

Issue - State: closed - Opened by EricSDavis over 1 year ago

#84 - Issue with plotting multiple signal tracks with plotMultiSignal

Issue - State: closed - Opened by mbond0718 over 1 year ago - 1 comment
Labels: bug

#83 - Intrachromosomal triangle plots?

Issue - State: open - Opened by ksmetz over 1 year ago - 6 comments
Labels: genome-wide🧬

#82 - Rotate plotGenes track vertically?

Issue - State: open - Opened by Irenexzwen over 1 year ago - 1 comment
Labels: enhancement

#81 - New function for annotating a genomic span

Issue - State: open - Opened by EricSDavis over 1 year ago
Labels: enhancement

#80 - Stripe annotations?

Issue - State: open - Opened by ksmetz over 1 year ago - 4 comments
Labels: enhancement

#79 - Overlayed bigwig tracks

Issue - State: closed - Opened by Knetsy almost 2 years ago - 4 comments

#78 - readHic only support some special resolution

Issue - State: closed - Opened by junjunlab almost 2 years ago - 2 comments

#76 - Plotting gene tracks with GENCODE annotations

Issue - State: closed - Opened by manuelfmerino almost 2 years ago - 2 comments

#75 - Fix mtfrm error

Pull Request - State: closed - Opened by EricSDavis almost 2 years ago

#74 - plotGenes: knownGene to refGene

Issue - State: closed - Opened by Kim-KL about 2 years ago - 4 comments

#73 - Rasterize

Issue - State: closed - Opened by Zepeng-Mu about 2 years ago - 3 comments

#72 - Copy Number feature request

Issue - State: open - Opened by jessicadlang about 2 years ago - 2 comments
Labels: enhancement

#71 - Plot names of bed and bedpe elements

Issue - State: open - Opened by ericahildebrand about 2 years ago - 1 comment
Labels: enhancement

#70 - More flexible colorby

Issue - State: open - Opened by Zepeng-Mu about 2 years ago - 2 comments
Labels: enhancement

#69 - `annoPixels()` does not annotate all pixels present in a rectangle HiC plot

Issue - State: closed - Opened by sarmapar about 2 years ago - 1 comment
Labels: bug

#68 - cannot install plotgardener on an M1 Mac

Issue - State: closed - Opened by a-g-robertson about 2 years ago - 4 comments

#67 - plotPairsArches: Line style

Issue - State: closed - Opened by Kim-KL about 2 years ago - 5 comments

#66 - plot .mcool format

Issue - State: closed - Opened by tamerbio over 2 years ago - 2 comments
Labels: enhancement

#65 - Error with plotGenes on custom genome

Issue - State: closed - Opened by rpolicastro over 2 years ago - 2 comments

#64 - Trouble installing plotgardner

Issue - State: closed - Opened by trb8 over 2 years ago

#63 - `mapColors` leads to downstream error in plotHic functions

Issue - State: closed - Opened by EricSDavis over 2 years ago
Labels: bug

#62 - Layout functions for row/column positions

Issue - State: closed - Opened by EricSDavis over 2 years ago
Labels: enhancement

#61 - plotPairsArches function

Issue - State: closed - Opened by artemyzhigulev over 2 years ago - 1 comment

#60 - plotranges inconsistent output

Issue - State: closed - Opened by jaclyn-marie over 2 years ago - 5 comments

#59 - Parameter to scale signals

Issue - State: closed - Opened by climouse over 2 years ago - 5 comments

#58 - Calling `pageGuideHide` causes the plot to be rendered twice for pdf output

Issue - State: closed - Opened by const-ae over 2 years ago - 3 comments
Labels: documentation

#57 - plotSignal help/error?

Issue - State: closed - Opened by jaclyn-marie over 2 years ago - 2 comments

#56 - Inverting domain annotations and clipping plotHicTriangle

Issue - State: closed - Opened by benayang almost 3 years ago - 3 comments

#55 - Color Ideogram bands

Issue - State: closed - Opened by mauerjh almost 3 years ago - 2 comments

#54 - Is there a way to highlight transcripts?

Issue - State: closed - Opened by davhum almost 3 years ago - 1 comment
Labels: enhancement

#53 - plotGenes and plotTranscripts fail with Drosophila dm6 assembly

Issue - State: closed - Opened by tjgibson almost 3 years ago - 3 comments

#52 - Potential issue plotting tracks with negative values

Issue - State: closed - Opened by adippolito12 almost 3 years ago - 1 comment

#51 - support for custome genome

Issue - State: closed - Opened by yinshiyi almost 3 years ago - 1 comment

#50 - clip parameter in `plotPairsArches( )`

Issue - State: closed - Opened by Rseq about 3 years ago - 4 comments

#49 - annoDomains( ) in plotHicRectangle( ) vs plotHicTriangle( )

Issue - State: closed - Opened by Rseq about 3 years ago - 2 comments

#48 - range limits on plotPairsArches

Issue - State: closed - Opened by Rseq about 3 years ago - 11 comments

#47 - Labeling enhancers

Issue - State: closed - Opened by jamesdalg about 3 years ago - 1 comment
Labels: enhancement

#46 - plotgardener issues on Windows in Bioc devel

Issue - State: closed - Opened by mikelove about 3 years ago - 3 comments
Labels: in progress

#45 - Title not appearing in legend

Issue - State: closed - Opened by EricSDavis about 3 years ago - 1 comment
Labels: bug

#44 - gene names disappear when zoomed out

Issue - State: closed - Opened by EricSDavis about 3 years ago - 2 comments
Labels: enhancement

#43 - Non model Organism support

Issue - State: closed - Opened by FabianGrammes about 3 years ago - 1 comment

#42 - Does plotgardener work with patchwork?

Issue - State: closed - Opened by soumitrakp over 3 years ago - 1 comment

#41 - plotGenes or plotTranscripts using a custom GTF file

Issue - State: closed - Opened by mmkim1210 over 3 years ago - 1 comment

#40 - plotSignal Error: Data ranges cannot overlap.

Issue - State: closed - Opened by Rseq over 3 years ago - 1 comment

#39 - assembly() with Refseq

Issue - State: closed - Opened by Rseq over 3 years ago - 1 comment

#38 - Support for interchromosomal matrices?

Issue - State: closed - Opened by joreynajr over 3 years ago - 3 comments
Labels: bug

#37 - Multi signal edits

Pull Request - State: closed - Opened by nekramer over 3 years ago

#36 - Custom genome

Issue - State: closed - Opened by KittJonathan over 3 years ago - 2 comments

#35 - inverted hic matrix

Issue - State: closed - Opened by fc-ibb105 over 3 years ago - 2 comments
Labels: enhancement

#27 - how to save the plots

Issue - State: closed - Opened by BenxiaHu almost 4 years ago - 4 comments