kdkorthauer/dmrseq

Issues

• Loading samples in new R takes too long time

  #68 opened 3 months ago by desmodus1984
  1

• Do no need "testCovariate"

  #67 opened 6 months ago by zhen-fu
  2

• read.bismark doesn't work.

  #65 opened 9 months ago by desmodus1984
  5

• Regarding CPU usage: it will fill up the entire server’s CPU.

  #66 opened 8 months ago by xuzhe010
  6

• Running block=TRUE crashes during permutations with "Error in .start_as_unnamed_integer(start)"

  #64 opened a year ago by mpiersonsmela
  8

• Volcano plot from dmrseq

  #59 opened 10 months ago by katkat-ri
  1

• How to produce dmrseq figure by defining specific gene symbol ?

  #54 opened 10 months ago by DengEr-1993
  3

• Can dmrseq be used on several groups but single sample in each group ?

  #63 opened a year ago by DengEr-1993
  1

• Can dmrseq be used on several groups but single sample in each group ?

  #62 opened a year ago by DengEr-1993
  0

• Error in (function (cond)

  #50 opened 2 years ago by dktanwar
  4

• Something wrong with the running of dmrseq()

  #61 opened a year ago by DengEr-1993
  3

• How to combinde several samples with different dimensions ?

  #60 opened a year ago by DengEr-1993
  2

• Question about Error "diff # of rows..." when running dmrseq

  #58 opened a year ago by KristenKrolick
  4

• adjustCovariate for a repeated measures two way ANOVA-like setup

  #56 opened a year ago by lars-work-sund
  4

• Could multiple groups compared be plotted in figure ?

  #55 opened 2 years ago by DengEr-1993
  3

• About plot feature: addPoints or not

  #53 opened 2 years ago by DengEr-1993
  2

• Error in meanDiff function

  #52 opened 2 years ago by delbala
  1

• Significance level with multiple pairwise comparisons

  #51 opened 2 years ago by SrenBlikdal
  2

• Error when running dmrseq function and question about generating PCA

  #38 opened 5 years ago by amjass12
  3

• Report a bug in parallel computation

  #49 opened 3 years ago by chengwenxuan1997
  2

• Changing y axis limits in plotDMRs

  #48 opened 3 years ago by hernandezvargash
  2

• Raw mean methylation difference vs smoothed scaled pooled proportion difference

  #47 opened 3 years ago by supermaxiste
  5

• Is it possible to output the smooth methylation estimates from dmrseq?

  #46 opened 3 years ago by seifudd
  2

• this tool could also be used in RRBS data or just WGBS?

  #45 opened 3 years ago by sixone11
  2

• block = TRUE with BiocParallel

  #44 opened 3 years ago by stephen-siecinski
  2

• Targeted Methyl-Seq

  #43 opened 3 years ago by hlkaatsch
  2

• distribution of coverage

  #40 opened 4 years ago by priyatamapandey
  1

• Possibility to visualize results of different values bpSpan

  #41 opened 4 years ago by tmms1
  2

• Conservativeness of test

  #39 opened 4 years ago by bazyliszek
  3

• Using dmrseq with other organisms and in a different methylation context.

  #34 opened 4 years ago by tmms1
  6

• Duration of a permutation longer than previous one

  #42 opened 4 years ago by tmms1
  3

• How to interpret beta and stat?

  #28 opened 5 years ago by bishwaG
  9

• A Bug in bumphunt(): cause index problems in chr2, chr10, chrX and chrM in dmrseq() results

  #37 opened 5 years ago by zyqfrog10
  6

• mcexit(0L) error

  #36 opened 5 years ago by zyqfrog10
  4

• ANOVA-like test for differences

  #35 opened 5 years ago by biobenkj
  2

• how to correctly set my testCovariate?

  #31 opened 5 years ago by MohamedRefaat92
  21

• Dmrseq parameters for short regions

  #33 opened 5 years ago by jckhearn
  1

• Running dmreseq using more than 1 core give an error

  #29 opened 5 years ago by MohamedRefaat92
  1

• MeDipSeq

  #32 opened 5 years ago by dktanwar
  1

• dmrseq fails while processing chromosomes/contigs

  #24 opened 5 years ago by jckhearn
  2

• Error in names(df2) <- paste0("beta_", levels(as.factor(dat$g.fac))[-1])

  #26 opened 6 years ago by MohamedRefaat92
  7

• Error: Biocparallel errors - element index: 1, 2, 3, 4, 5, 6...

  #27 opened 6 years ago by sebcomarmond
  3

• names do not match previous names

  #25 opened 6 years ago by fhalbritter
  3

• DMRseq stops after processing a few chromosome

  #23 opened 6 years ago by geethavenk
  8

• Error when the test covariate has more than two levels

  #22 opened 6 years ago by RoseString
  5

• Multiple cores don't reduce running time

  #21 opened 6 years ago by ingobulla
  3

• Large q-values

  #19 opened 6 years ago by RoseString
  6

• Feature request: `compareTrack` more than 4

  #18 opened 6 years ago by dktanwar
  1

• Only returning 2 columns for multiple conditions in a single testCovariate

  #20 opened 6 years ago by jrhawley
  2

• Can dmrseq be used on single CpG sites?

  #17 opened 6 years ago by Geetharv
  1