kdkorthauer dmrseq issues

kdkorthauer / dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

MIT License

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issues

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Do no need "testCovariate"

#67 zhen-fu closed 1 week ago
2
Regarding CPU usage: it will fill up the entire server’s CPU.

#66 xuzhe010 closed 2 months ago
6
read.bismark doesn't work.

#65 desmodus1984 closed 2 months ago
5
Running block=TRUE crashes during permutations with "Error in .start_as_unnamed_integer(start)"

#64 mpiersonsmela opened 5 months ago
8
Can dmrseq be used on several groups but single sample in each group ?

#63 DengEr-1993 closed 6 months ago
1
Can dmrseq be used on several groups but single sample in each group ?

#62 DengEr-1993 closed 6 months ago
0
Something wrong with the running of dmrseq()

#61 DengEr-1993 closed 6 months ago
3
How to combinde several samples with different dimensions ?

#60 DengEr-1993 closed 6 months ago
2
Volcano plot from dmrseq

#59 katkat-ri closed 4 months ago
1
Question about Error "diff # of rows..." when running dmrseq

#58 KristenKrolick closed 7 months ago
4
Add missing `Suggests` entries

#57 martin-g closed 11 months ago
3
adjustCovariate for a repeated measures two way ANOVA-like setup

#56 lars-work-sund closed 11 months ago
4
Could multiple groups compared be plotted in figure ?

#55 DengEr-1993 closed 1 year ago
3
How to produce dmrseq figure by defining specific gene symbol ?

#54 DengEr-1993 closed 4 months ago
3
About plot feature: addPoints or not

#53 DengEr-1993 closed 1 year ago
2
Error in meanDiff function

#52 delbala closed 1 year ago
1
Significance level with multiple pairwise comparisons

#51 SrenBlikdal closed 1 year ago
2
Error in (function (cond)

#50 dktanwar closed 1 year ago
4
Report a bug in parallel computation

#49 chengwenxuan1997 closed 2 years ago
2
Changing y axis limits in plotDMRs

#48 hernandezvargash opened 2 years ago
2
Raw mean methylation difference vs smoothed scaled pooled proportion difference

#47 supermaxiste closed 2 years ago
5
Is it possible to output the smooth methylation estimates from dmrseq?

#46 seifudd closed 2 years ago
2
this tool could also be used in RRBS data or just WGBS?

#45 sixone11 closed 2 years ago
2
block = TRUE with BiocParallel

#44 stephen-siecinski closed 2 years ago
2
Targeted Methyl-Seq

#43 hlkaatsch closed 2 years ago
2
Duration of a permutation longer than previous one

#42 tmms1 opened 3 years ago
3
Possibility to visualize results of different values bpSpan

#41 tmms1 closed 3 years ago
2
distribution of coverage

#40 priyatamapandey closed 3 years ago
1
Conservativeness of test

#39 bazyliszek closed 3 years ago
3
Error when running dmrseq function and question about generating PCA

#38 amjass12 opened 4 years ago
3
A Bug in bumphunt(): cause index problems in chr2, chr10, chrX and chrM in dmrseq() results

#37 zyqfrog10 closed 4 years ago
6
mcexit(0L) error

#36 zyqfrog10 closed 4 years ago
4
ANOVA-like test for differences

#35 biobenkj closed 4 years ago
2
Using dmrseq with other organisms and in a different methylation context.

#34 tmms1 closed 3 years ago
6
Dmrseq parameters for short regions

#33 jckhearn closed 4 years ago
1
MeDipSeq

#32 dktanwar closed 4 years ago
1
how to correctly set my testCovariate?

#31 MohamedRefaat92 closed 4 years ago
21
fixed small typos

#30 stephaniehicks closed 4 years ago
1
Running dmreseq using more than 1 core give an error

#29 MohamedRefaat92 closed 4 years ago
1
How to interpret beta and stat?

#28 bishwaG closed 4 years ago
9
Error: Biocparallel errors - element index: 1, 2, 3, 4, 5, 6...

#27 sebcomarmond closed 5 years ago
3
Error in names(df2) <- paste0("beta_", levels(as.factor(dat$g.fac))[-1])

#26 MohamedRefaat92 closed 5 years ago
7
names do not match previous names

#25 fhalbritter closed 5 years ago
3
dmrseq fails while processing chromosomes/contigs

#24 jckhearn closed 4 years ago
2
DMRseq stops after processing a few chromosome

#23 geethavenk closed 5 years ago
8
Error when the test covariate has more than two levels

#22 RoseString closed 5 years ago
5
Multiple cores don't reduce running time

#21 ingobulla closed 5 years ago
3
Only returning 2 columns for multiple conditions in a single testCovariate

#20 jrhawley closed 5 years ago
2
Large q-values

#19 RoseString closed 5 years ago
6
Feature request: `compareTrack` more than 4

#18 dktanwar closed 5 years ago
1