HenrikBengtsson PSCBS issues

HenrikBengtsson / PSCBS

🔬 R package: Analysis of Parent-Specific DNA Copy Numbers

https://cran.r-project.org/package=PSCBS

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issues

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The 'PairedPSCBS.tex.rsp' vignettes requires the Hmisc package

#66 HenrikBengtsson closed 2 years ago
1
example("segmentByNonPairedPSCBS") requires the Hmisc package

#65 HenrikBengtsson closed 2 years ago
1
Error in calling AB in unpaired mode

#64 hannanw opened 3 years ago
1
Error in Calling NTCN in Paired mode

#63 hannanw opened 3 years ago
3
README: Update installation instructions on Bioconductor dependencies

#62 HenrikBengtsson closed 2 years ago
1
CLEANUP: Deprecate load() and save() for AbstractCBS

#61 HenrikBengtsson closed 3 years ago
0
RNG issues when segmenting with predefined segments, e.g. chromosome args

#60 HenrikBengtsson closed 2 years ago
1
Update CITATION with "unsafe" URL

#59 HenrikBengtsson closed 3 years ago
0
CLEANUP: Stop testing against deprecated future.BatchJobs

#58 HenrikBengtsson closed 3 years ago
0
ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [rbind]

#57 HenrikBengtsson closed 3 years ago
1
ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [data.frame]

#56 HenrikBengtsson closed 3 years ago
1
trouble installing PSCBS

#55 markrobinsonuzh closed 4 years ago
3
CLEANUP: Import throw() from R.oo (>= 1.23.0)

#54 HenrikBengtsson closed 4 years ago
0
Strange CBS failure with no calls for an entire chromosome

#53 arostamianfar closed 4 years ago
2
Segments outside of ylim are not seen

#52 HenrikBengtsson opened 5 years ago
0
BUG: 'length(x) = 5 > 1' in coercion to 'logical(1)' - R CMD check++

#51 HenrikBengtsson closed 5 years ago
1
ROBUSTNESS: report() for PairedPSCBS may fail if not enough data points

#50 HenrikBengtsson closed 5 years ago
1
Add dnacopy weighting

#49 lima1 opened 5 years ago
4
New CRAN release before Bioc 3.8

#48 lima1 closed 6 years ago
6
Dropped semicolon at end of line

#47 gara-z closed 6 years ago
1
SPEEDUP: base::stopifnot() -> stop_if_not()

#46 HenrikBengtsson closed 6 years ago
0
CLEANUP: drop argument 'preserveScale' from segmentByPairedPSCBS()

#45 HenrikBengtsson closed 6 years ago
1
"Normal contamination": Argument for promoting our "secret" estimateKappa()

#44 HenrikBengtsson closed 5 years ago
3
plotTracks() for multi-chromosome CBS objects gives error on "Argument 'Clim' is not a vector: NULL"

#43 HenrikBengtsson closed 6 years ago
2
subset(), head() and tail() based on segments

#42 HenrikBengtsson opened 6 years ago
1
CLEANUP: stray code?

#41 HenrikBengtsson closed 6 years ago
0
CLEANUP: replace append() with c() or rbind()

#40 HenrikBengtsson closed 6 years ago
0
CLEANUP: remove defunct functions

#39 HenrikBengtsson closed 6 years ago
0
SPEEDUP: Profile to find bottlenecks

#38 HenrikBengtsson closed 6 years ago
1
Move aroma.light to Imports from Suggests

#37 HenrikBengtsson closed 7 years ago
0
TESTS: Remove test with future::plan(lazy), which is deprecated and will be defunct soon

#36 HenrikBengtsson closed 7 years ago
1
PSCBS - segmentation

#35 ramaniak closed 7 years ago
2
Paired PSCBS - Error running call NTCN

#34 gaiusjaugustus closed 7 years ago
1
SPEEDUP: Parallelize bootstrapSegmentsAndChangepoints()

#33 HenrikBengtsson opened 8 years ago
1
FUTURES: tests/segmentByPairedPSCBS,calls.R gives different results with lazy and eager futures

#32 HenrikBengtsson closed 8 years ago
2
METACRAN: Keep README.md so it appears on METACRAN

#31 HenrikBengtsson closed 7 years ago
0
PARALLEL: Reproducibility and random seeds

#30 HenrikBengtsson closed 8 years ago
3
segmentByCBS(..., w=w, knownSegments=segs) gives error on 'weights' if segments has zero loci

#29 HenrikBengtsson closed 8 years ago
1
segmentByCBS(..., w=w, knownSegments=segs) gives validation error

#28 HenrikBengtsson closed 8 years ago
1
Make preserveScale=FALSE the default

#27 HenrikBengtsson closed 8 years ago
1
Add support for weights to segmentByPairedPSCBS()

#26 HenrikBengtsson opened 8 years ago
5
joinSegments() does not work with multiple chromosomes

#25 HenrikBengtsson closed 9 years ago
0
Add as.CBS() for CBS and PSCBS

#24 HenrikBengtsson closed 9 years ago
1
Import all functions

#23 HenrikBengtsson closed 9 years ago
0
PARALLEL: Make use of futures

#22 HenrikBengtsson closed 8 years ago
4
Add writeWIG() for CBS objects

#21 HenrikBengtsson closed 9 years ago
2
`pruneBySdUndo()` does not work on multiple chromosomes(?)

#20 HenrikBengtsson closed 9 years ago
1
segmentByCBS() identifies segment of length one (zero?) with same start position as next one

#19 HenrikBengtsson closed 8 years ago
5
segmentByCBS(..., w=...): Resulting mean levels are calculated without using weights 'w'

#18 HenrikBengtsson closed 9 years ago
5
segmentCBS(): Add argument 'flavor' for segment under different transforms

#17 HenrikBengtsson opened 9 years ago
0