Ecosyste.ms: Issues

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GitHub / HenrikBengtsson/PSCBS issues and pull requests

#66 - The 'PairedPSCBS.tex.rsp' vignettes requires the Hmisc package

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

#65 - example("segmentByNonPairedPSCBS") requires the Hmisc package

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

#64 - Error in calling AB in unpaired mode

Issue - State: open - Opened by hannanw about 3 years ago - 1 comment
Labels: bug, question

#63 - Error in Calling NTCN in Paired mode

Issue - State: open - Opened by hannanw about 3 years ago - 3 comments
Labels: question

#62 - README: Update installation instructions on Bioconductor dependencies

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

#61 - CLEANUP: Deprecate load() and save() for AbstractCBS

Issue - State: closed - Opened by HenrikBengtsson over 3 years ago

#60 - RNG issues when segmenting with predefined segments, e.g. chromosome args

Issue - State: closed - Opened by HenrikBengtsson over 3 years ago - 1 comment
Labels: bug

#59 - Update CITATION with "unsafe" URL

Issue - State: closed - Opened by HenrikBengtsson almost 4 years ago

#58 - CLEANUP: Stop testing against deprecated future.BatchJobs

Issue - State: closed - Opened by HenrikBengtsson almost 4 years ago

#57 - ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [rbind]

Issue - State: closed - Opened by HenrikBengtsson over 4 years ago - 1 comment
Labels: wontfix

#56 - ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame]

Issue - State: closed - Opened by HenrikBengtsson over 4 years ago - 1 comment
Labels: wontfix

#55 - trouble installing PSCBS

Issue - State: closed - Opened by markrobinsonuzh over 4 years ago - 3 comments

#54 - CLEANUP: Import throw() from R.oo (>= 1.23.0)

Issue - State: closed - Opened by HenrikBengtsson about 5 years ago

#53 - Strange CBS failure with no calls for an entire chromosome

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

#52 - Segments outside of ylim are not seen

Issue - State: open - Opened by HenrikBengtsson over 5 years ago

#51 - BUG: 'length(x) = 5 > 1' in coercion to 'logical(1)' - R CMD check++

Issue - State: closed - Opened by HenrikBengtsson over 5 years ago - 1 comment
Labels: bug

#50 - ROBUSTNESS: report() for PairedPSCBS may fail if not enough data points

Issue - State: closed - Opened by HenrikBengtsson almost 6 years ago - 1 comment
Labels: bug

#49 - Add dnacopy weighting

Pull Request - State: open - Opened by lima1 about 6 years ago - 4 comments

#48 - New CRAN release before Bioc 3.8

Issue - State: closed - Opened by lima1 over 6 years ago - 6 comments

#47 - Dropped semicolon at end of line

Pull Request - State: closed - Opened by gara-z over 6 years ago - 1 comment

#46 - SPEEDUP: base::stopifnot() -> stop_if_not()

Issue - State: closed - Opened by HenrikBengtsson over 6 years ago

#45 - CLEANUP: drop argument 'preserveScale' from segmentByPairedPSCBS()

Issue - State: closed - Opened by HenrikBengtsson over 6 years ago - 1 comment

#44 - "Normal contamination": Argument for promoting our "secret" estimateKappa()

Issue - State: closed - Opened by HenrikBengtsson over 6 years ago - 3 comments
Labels: enhancement

#42 - subset(), head() and tail() based on segments

Issue - State: open - Opened by HenrikBengtsson almost 7 years ago - 1 comment
Labels: enhancement

#41 - CLEANUP: stray code?

Issue - State: closed - Opened by HenrikBengtsson almost 7 years ago

#40 - CLEANUP: replace append() with c() or rbind()

Issue - State: closed - Opened by HenrikBengtsson almost 7 years ago

#39 - CLEANUP: remove defunct functions

Issue - State: closed - Opened by HenrikBengtsson almost 7 years ago

#38 - SPEEDUP: Profile to find bottlenecks

Issue - State: closed - Opened by HenrikBengtsson almost 7 years ago - 1 comment

#37 - Move aroma.light to Imports from Suggests

Issue - State: closed - Opened by HenrikBengtsson over 7 years ago

#35 - PSCBS - segmentation

Issue - State: closed - Opened by ramaniak almost 8 years ago - 2 comments

#34 - Paired PSCBS - Error running call NTCN

Issue - State: closed - Opened by gaiusjaugustus over 8 years ago - 1 comment

#33 - SPEEDUP: Parallelize bootstrapSegmentsAndChangepoints()

Issue - State: open - Opened by HenrikBengtsson over 8 years ago - 1 comment
Labels: enhancement

#32 - FUTURES: tests/segmentByPairedPSCBS,calls.R gives different results with lazy and eager futures

Issue - State: closed - Opened by HenrikBengtsson almost 9 years ago - 2 comments
Labels: bug, help wanted

#31 - METACRAN: Keep README.md so it appears on METACRAN

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago
Labels: enhancement

#30 - PARALLEL: Reproducibility and random seeds

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago - 3 comments
Labels: enhancement, help wanted

#28 - segmentByCBS(..., w=w, knownSegments=segs) gives validation error

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago - 1 comment
Labels: bug

#27 - Make preserveScale=FALSE the default

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago - 1 comment
Labels: enhancement

#26 - Add support for weights to segmentByPairedPSCBS()

Issue - State: open - Opened by HenrikBengtsson about 9 years ago - 5 comments
Labels: enhancement

#25 - joinSegments() does not work with multiple chromosomes

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago
Labels: bug

#24 - Add as.CBS() for CBS and PSCBS

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago - 1 comment
Labels: enhancement, wontfix

#23 - Import all functions

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago
Labels: bug, help wanted, CRAN Policy

#22 - PARALLEL: Make use of futures

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago - 4 comments
Labels: enhancement

#21 - Add writeWIG() for CBS objects

Issue - State: closed - Opened by HenrikBengtsson about 9 years ago - 2 comments
Labels: enhancement

#20 - `pruneBySdUndo()` does not work on multiple chromosomes(?)

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 1 comment
Labels: bug, help wanted

#19 - segmentByCBS() identifies segment of length one (zero?) with same start position as next one

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 5 comments
Labels: bug, help wanted

#18 - segmentByCBS(..., w=...): Resulting mean levels are calculated without using weights 'w'

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 5 comments
Labels: bug

#17 - segmentCBS(): Add argument 'flavor' for segment under different transforms

Issue - State: open - Opened by HenrikBengtsson over 9 years ago
Labels: enhancement

#16 - segmentByCBS(): Add argument 'avg'

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 3 comments
Labels: enhancement

#15 - Is default 'knownSegments' for segmentByCBS() correct?

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 1 comment
Labels: help wanted, question

#14 - segmentByPairedPSCBS(): Is `flavor` with `sqrt(tcn)` really implemented?

Issue - State: open - Opened by HenrikBengtsson over 9 years ago
Labels: bug, help wanted

#13 - segmentByPairedPSCBS(): Add support to identify breakpoints on log(tcn) scale

Issue - State: open - Opened by HenrikBengtsson over 9 years ago
Labels: enhancement, help wanted

#12 - segmentByPairedPSCBS() with betaTN should not give an error about `tbn=TRUE`

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 2 comments
Labels: enhancement, help wanted

#11 - segmentByPairedPSCBS() should also accept (TCN,DH) signals

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago
Labels: enhancement, help wanted

#10 - Add na.rm=TRUE to findLargeGaps()

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 1 comment
Labels: wontfix

#9 - gapsToSegments() assumes at least one gap

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago
Labels: bug, help wanted

#8 - findLargeGaps() can return negative length gaps

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 1 comment
Labels: bug, help wanted

#7 - gapsToSegments() requires 'chromosome' but findLargeGaps() doesn't

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago
Labels: bug, help wanted

#6 - BUG: findLargeGaps() can return NULL; should always be zero-row data.frame

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 1 comment
Labels: bug, help wanted

#5 - WISH: Plotting raw data pre-segmentation

Issue - State: open - Opened by HenrikBengtsson over 9 years ago
Labels: enhancement

#4 - report() should return an RspFileProduct

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago - 1 comment
Labels: enhancement

#3 - pruneByHClust(): Not working for multiple chromosomes?

Issue - State: closed - Opened by HenrikBengtsson over 9 years ago
Labels: bug, enhancement

#2 - Vignettes: Use multiple \VignetteKeyword{}:s instead of a single one with commas

Issue - State: closed - Opened by HenrikBengtsson almost 10 years ago - 1 comment
Labels: help wanted, CRAN Policy

#1 - Update package title to use Title Case

Issue - State: closed - Opened by HenrikBengtsson almost 10 years ago - 1 comment
Labels: CRAN Policy