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al2na
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methylKit
R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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Fix bedgraph error due to NA handling in meth.diff export
#332
alexg9010
closed
4 days ago
0
Error in testthat due to NA handling in test-17-bedgraph.r when exporting meth.diff as log-transformed value
#331
alexg9010
closed
4 days ago
0
Error: The sam file is not sorted properly on positions
#330
iranianuser
closed
1 month ago
10
gene bed files requirement for annotation
#329
LeilyR
closed
1 month ago
1
Extract the most differentially methylated genes
#328
AlbanZimmer
opened
2 months ago
0
uneven number of replicates
#327
LandiMi2
closed
2 weeks ago
2
Issue in unite funtion
#326
Anjaligarg006
opened
3 months ago
7
【question】about the coverage in processBismarkAln
#325
lilwo
closed
3 months ago
2
how to use the methylation data when to do boxplot ?
#324
DengEr-1993
opened
3 months ago
4
NA values
#323
Silvia-Giorgia-Signorini
opened
4 months ago
1
Support for all context all types of methylation data
#322
Ge0rges
opened
6 months ago
0
regioncounts lost some regions
#321
leon945945
closed
5 months ago
4
tileMethylCounts(mrl_base, win.size=600,step.size=200,cov.bases = 4
#320
yhj-j
closed
7 months ago
1
PCASamples options
#319
Hannah1746
closed
7 months ago
1
error：Calls: calculateDiffMeth ... simplify2array -> mclapply -> lapply -> FUN -> mcfork
#318
changchuanjun
closed
7 months ago
2
MethylationStats shows one peak
#317
gevro
closed
8 months ago
6
cannot find -lrtmp
#316
GuoanQi1996
closed
8 months ago
2
filter by chromosome
#315
gevro
closed
8 months ago
1
One question about DMR calling between single sample in one group versus replicated sample in another group
#314
DengEr-1993
closed
8 months ago
4
percMethylation does not reach 100%
#313
SophieValk
closed
9 months ago
3
Typo in vignette
#312
llrs
opened
10 months ago
0
Refactor_loading_tabix
#311
alexg9010
opened
10 months ago
0
Fix rdevel build
#310
alexg9010
closed
10 months ago
0
Fix bioc R-devel build issue
#309
alexg9010
closed
10 months ago
3
MethylKit and Methylation Data from PacBio sequence
#308
olaraym
closed
10 months ago
2
The deep theory of calculateDiffMeth() function of MethylKit
#307
DengEr-1993
closed
10 months ago
4
error in getTargetAnnotationStats
#306
Kaustav-93
closed
8 months ago
1
Illegal operation when opening BiocGenerics
#305
desmodus1984
closed
8 months ago
3
Data.frame error during differential methylation with covariate.
#304
desmodus1984
closed
8 months ago
7
Interpreting the CpG pearson correlation plot
#303
bioinfo23
closed
10 months ago
3
Error reading in file
#302
Ge0rges
opened
1 year ago
3
Annotate DMRs with .gff files?
#301
Ge0rges
closed
1 year ago
2
Correct way to read in modkit bedmethyl file?
#300
Ge0rges
closed
1 year ago
3
methRead Problem as "the condition has length > 1"
#299
Ziwei-Liu
closed
1 year ago
1
Filtering by SD after unite, by group; covariate in beta-binomial model
#298
desmodus1984
closed
1 year ago
3
min.per.group in unite() --> NA values appear --> row counts = NULL
#297
mirurb
closed
1 year ago
2
methylKit "unite" function error message
#296
mirurb
opened
1 year ago
5
Installation Error - R/Conda
#295
desmodus1984
closed
3 weeks ago
1
Is it necessary that using normalization before doing dmr calling ?
#294
DengEr-1993
closed
1 year ago
3
Reading BedGraph file using methRead()
#293
ANGEL-D-SAMUEL
closed
1 year ago
1
add 'chunk' option for getData
#292
RJDan
opened
1 year ago
2
If there is a parameter which can be used to determine how many CpG site (not Coverage on one CpG site) will be tiled together ?
#291
DengEr-1993
closed
1 year ago
6
Error during methylkit unite
#290
manjumoorthy95
opened
1 year ago
1
Could methylKit be used to compare one group with the other one group which was merged by mulitple groups ?
#289
DengEr-1993
closed
1 year ago
3
check for duplicated regions in regioncounts
#288
alexg9010
opened
1 year ago
0
Some feedback and suggestions for Methykit package
#287
SEvisual
opened
1 year ago
1
Import CpG_context file to Methylkit
#286
manjumoorthy95
closed
1 year ago
3
Which parameter determined the p value and q value but doesn't change the meth.diff ?
#285
DengEr-1993
closed
1 year ago
1
It seems sth wrong with calculateDiffMeth() and getMethyDiff() in MethylKit
#284
DengEr-1993
closed
1 year ago
10
unite() function reassigns sample ID's
#283
laurahspencer
closed
1 year ago
7
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