ccagc/QDNAseq issues and pull requests

#130 - poolRuns() error, invalid 'row.names' length

Issue - State: open - Opened by jppmatos 5 months ago

#129 - Next release

Issue - State: closed - Opened by HenrikBengtsson 6 months ago

#128 - Blacklisted regions in applyFilter function without providing a bed file

Issue - State: open - Opened by alexvasilikop 6 months ago

#127 - Genome build hg38

Issue - State: open - Opened by henryone0910 9 months ago

#126 - Genome for mm39

Issue - State: open - Opened by tashaann 9 months ago

#125 - T2T genome support

Issue - State: open - Opened by liuyangzzu 9 months ago

#124 - poolRuns() error or misapplication

Issue - State: closed - Opened by jppmatos 11 months ago - 7 comments

#123 - R CMD check: Sporadic test errors; Error in diff2(x, differences = diff) : names() applied to a non-vector

Issue - State: open - Opened by HenrikBengtsson 11 months ago - 3 comments

#122 - Is there a way to hack QDNAseq plot methods to plot a point on the log2 ratio plots?

Issue - State: open - Opened by zetamui 12 months ago - 1 comment

#121 - Output VCF is not valid due to symbolic allele used as reference allele

Issue - State: open - Opened by vlshesketh about 1 year ago - 6 comments
Labels: help wanted

#120 - END INFO sub-field not documented in VCF Header

Issue - State: closed - Opened by cjw85 about 1 year ago - 3 comments

#119 - Marmoset bin annotation creation challenge

Issue - State: open - Opened by kojimak324 about 1 year ago

#118 - Downloading 1000 Genomes samples is inactive

Issue - State: open - Opened by kojimak324 about 1 year ago

#117 - Extracting reads from bam file using binReadCounts takes too long

Issue - State: open - Opened by Urja25 over 1 year ago - 2 comments
Labels: question

#116 - How can I merge binReadCounts results?

Issue - State: open - Opened by hd00ljy almost 2 years ago

#115 - Patch 1 - user defined segment led

Pull Request - State: open - Opened by RodrigoGM almost 2 years ago

#114 - exportBins to seg/vcf doesn't contain all calls

Issue - State: open - Opened by helaersr almost 2 years ago

#113 - exportBins

Issue - State: closed - Opened by lightowlers almost 2 years ago - 1 comment

#112 - error with poolRuns

Issue - State: closed - Opened by jpoell about 2 years ago - 7 comments
Labels: bug

#111 - QDNAseq 1st time issues

Issue - State: open - Opened by RMParkes about 2 years ago

#110 - Directly loading counts matrix

Issue - State: open - Opened by shashwatsahay over 2 years ago
Labels: question

#109 - CODE: if() conditions comparing class() to string

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

#108 - Export Noise Plot data

Issue - State: open - Opened by hannesbecher almost 3 years ago

#107 - Export segements and calls to same BED file

Issue - State: open - Opened by hannesbecher almost 3 years ago

#106 - Prevent data.frames from turning into vectors

Pull Request - State: open - Opened by ilarischeinin almost 3 years ago - 1 comment

#105 - Error in e2[[j]]: subscript out of bounds

Issue - State: open - Opened by RodrigoGM almost 3 years ago - 1 comment
Labels: CGHcall package

#104 - Running QDNAseq on WES data

Issue - State: open - Opened by palakpatel09 almost 3 years ago - 1 comment

#103 - adjust the width/height of the CNV plot

Issue - State: open - Opened by asaki1986 almost 3 years ago

#102 - exportBins to seg/vcf when one or zero CNV are called

Issue - State: open - Opened by helaersr almost 3 years ago - 9 comments
Labels: bug, help wanted

#101 - WISH: Update binReadCounts() to read in chunks by default

Issue - State: open - Opened by HenrikBengtsson about 3 years ago

#100 - 'Realloc' could not re-allocate memory

Issue - State: closed - Opened by helaersr about 3 years ago - 7 comments

#99 - error on calculateBlacklist

Issue - State: open - Opened by briverog about 3 years ago

#98 - SPEEDUP: Use useNames=FALSE for all matrixStats calls

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

#97 - CLEANUP: Move 'future' to Suggests

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

#96 - Reproducible results?

Issue - State: closed - Opened by sxv over 3 years ago - 3 comments
Labels: question, help wanted

#95 - BUG: exportBins() corrupts options 'scipen' on exit

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

#94 - Make exportBins() return pathnames of files written

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

#93 - BUG: `exportBins()` with `format = "seg"` or `format = "vcf"` does not respect argument `file`

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

#92 - Recycling array of length 1 in vector-array arithmetic is deprecated. Use c() or as.vector() instead.

Issue - State: closed - Opened by sxv over 3 years ago - 3 comments
Labels: invalid, CGHcall package

#91 - Filter by region of chromosome

Issue - State: open - Opened by HJeffery over 3 years ago

#90 - prevent rle combining across no copynumber change

Pull Request - State: closed - Opened by RoelKluin over 3 years ago - 5 comments

#89 - binReadCounts fails when setting chunksize

Issue - State: closed - Opened by SebastianHollizeck almost 4 years ago - 5 comments
Labels: bug

#88 - exportBins does log2 transform even on data formats it should not do

Issue - State: closed - Opened by lbeltrame over 4 years ago - 2 comments
Labels: bug

#87 - exportBins errors

Issue - State: closed - Opened by mmterpstra over 4 years ago - 10 comments
Labels: bug

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

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

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

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

#84 - ROBUSTNESS: Add explicit 'stringsAsFactors' arguments [read.table]

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

#83 - poolRuns colMeans2 error

Issue - State: closed - Opened by srinew about 5 years ago - 1 comment

#82 - compareToReference handles zeroes in reference poorly

Issue - State: open - Opened by JocelynSP about 5 years ago

#81 - getBinAnnotations: Error in download.file

Issue - State: closed - Opened by ilarischeinin over 5 years ago
Labels: wontfix

#80 - VIGNETTE: Broken links/URL

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