ccagc QDNAseq issues - Githubissues

ccagc / QDNAseq

QDNAseq package for Bioconductor

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VIGNETTE: Broken links/URL

#80 HenrikBengtsson opened 5 years ago
5
callBins() produce some print() output

#79 HenrikBengtsson closed 5 years ago
1
exportBins() uses print() to output a warning

#78 HenrikBengtsson closed 5 years ago
0
OUTPUT NOISE: Add argument 'verbose' to all functions

#77 HenrikBengtsson closed 5 years ago
0
CLEANUP: Replace single usage of BiocParallel::bpapply() with future.apply::future_lapply()

#76 HenrikBengtsson closed 5 years ago
0
OUTPUT NOISE: callBins() produces lots of outputs

#75 HenrikBengtsson closed 5 years ago
1
PERFORMANCE: rowSums(x[, cols]) -> matrixStats::rowSums2(x, cols=cols)

#74 HenrikBengtsson closed 5 years ago
0
PR: Add back PR #61

#73 HenrikBengtsson closed 5 years ago
0
TESTS: Add package tests on parallel processing

#72 HenrikBengtsson closed 5 years ago
0
PERFORMANCE: Unnecessary coercions

#71 HenrikBengtsson closed 5 years ago
0
DOCS: parallel section is dated

#70 HenrikBengtsson closed 5 years ago
0
ROBUSTNESS: Use TRUE/FALSE - not T/F

#69 HenrikBengtsson closed 5 years ago
0
CLEANUP: Can now make use of future.apply()

#68 HenrikBengtsson closed 5 years ago
2
CLEANUP: Retire AWS S3 annotation data in favor of QDNAseq.{{genome}} packages

#67 HenrikBengtsson closed 5 years ago
3
R CMD check WARNING: "Undocumented code objects: ‘exportVCF’"

#66 HenrikBengtsson closed 5 years ago
1
Travis CI: Errors because the .travis.yml file is rather dated

#65 HenrikBengtsson closed 5 years ago
1
Syncing with Bioconductor Git repository

#64 HenrikBengtsson closed 5 years ago
3
mutiple ref while using "compareToReference"

#63 jiading opened 5 years ago
1
Problems with exportVCF function

#62 LanyingWei closed 3 years ago
2
Now correctly plots segment values above and below ylim)

#61 edk360 closed 5 years ago
4
added conditional argument to include zeros in .seg output

#60 RodrigoGM closed 5 years ago
0
QDNAseq.hg38: Bin annotation for hg38?

#59 nikleotide opened 5 years ago
33
Length of 'dimnames' [2] not equal to array extent

#58 RodrigoGM closed 5 years ago
3
hg38 compatibility

#57 sxv closed 5 years ago
3
The vcf file report false length of variant

#56 Riverzrw closed 3 years ago
1
How to extract copy number aberrations

#55 ghost closed 3 years ago
3
BAM of single chromosome but plot() plots all chromosomes

#54 bibbers93 closed 6 years ago
2
Changed cbind to data.frame call in calculateBlacklistByRegions function

#53 marcjwilliams1 closed 5 years ago
0
Question: Does one need to sort input BAM files?

#52 rgranit opened 6 years ago
0
applyFilters: residual 4.0 standard deviations

#51 funnell opened 6 years ago
0
Downloads of PE100 bin annotations

#50 lbeltrame opened 6 years ago
3
segmentBins() prints NA, leading to failures

#49 argymeg closed 2 years ago
10
Residual filter missing for chromosomes

#48 mahmadza opened 6 years ago
3
Export calls in vcf format

#47 ctrnsntx closed 3 years ago
1
Failed to infer inheritance of QDNAseqSignals when running with Rscript

#46 biocyberman closed 6 years ago
2
Cleanup some nits

#45 sambrightman closed 5 years ago
2
Parallelize binReadCounts by chromosome when chunkSize is used

#44 sambrightman closed 7 years ago
3
QDNAseq support for .cram files

#43 matthdsm closed 6 years ago
1
binReadCounts; argument "bx" is missing

#42 u0054600 closed 8 years ago
3
Prepare for update in matrixStats where colMedians() is no longer an S4 method

#41 HenrikBengtsson closed 8 years ago
12
Prepare for update in matrixStats where colMedians() is no longer an S4 method

#40 HenrikBengtsson closed 8 years ago
1
Add importFrom("stats", "formula")

#39 HenrikBengtsson closed 8 years ago
1
number of reads in the bins

#38 jiading closed 8 years ago
1
compareToReference Error

#37 jiading closed 8 years ago
5
detect <3M CNVs by adjust alpha?

#36 jiading closed 8 years ago
3
Expected & measured SD

#35 jiading closed 8 years ago
2
Error msg of applyFilters(.... chromosomes=NA)

#34 jiading closed 8 years ago
5
Push 1.9.1 to Bioconductor

#33 ilarischeinin closed 8 years ago
2
Fixing remaining R CMD check NOTE and bumping package dependencies

#32 HenrikBengtsson closed 8 years ago
4
Generating bin annotations for chrX..

#31 johali closed 8 years ago
6

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