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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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Is this repo still relevant?
#276
hukai916
closed
1 year ago
1
unite function error
#275
mohsennabian
closed
1 year ago
1
Re-Assignment of Sample Ids fails
#274
alexg9010
opened
1 year ago
0
References are not rendered in vignette
#273
alexg9010
opened
1 year ago
0
Verify content of file passed to methRead
#272
alexg9010
opened
1 year ago
0
uniting objects with "base" resolution and strand "*" breaks when requesting destranding
#271
alexg9010
opened
1 year ago
1
uniting methylRawDB objects with regional resolution and setting destrand=TRUE deletes the original objects
#270
alexg9010
opened
1 year ago
1
segfault when uniting large methylrawlistDB object
#269
ethan-shealy
opened
1 year ago
2
Actions bioc
#268
alexg9010
closed
1 year ago
0
add github actions Standard CI workflow
#267
alexg9010
closed
1 year ago
0
dbdir= argument from tilemethylCounts(), does not work with methylRawListDB data
#266
AnjaCaRa
opened
1 year ago
1
Error in calculateDiffMeth with dispersion=MN
#265
alynn1993
opened
2 years ago
1
simData for regions
#264
malonzm1
closed
2 years ago
4
How to merge when reading multiple files using readMethylDB?
#263
coffeeCowLu
closed
1 year ago
1
Error when running MethSeg
#262
nnlrl
closed
2 years ago
2
How does calculateDiffMeth cope with multiple treatment groups (>2) ?
#261
erikras12
closed
1 year ago
1
How to use methyKit with two platform data with different coverage distribution
#260
liuyangzzu
opened
2 years ago
2
Minor corrections
#259
GhislainFievet
opened
2 years ago
0
Function for converting Granges to Methylkit Object
#258
hchetia
closed
2 years ago
7
Clarifications on filterByCoverage
#257
franrodalg
closed
2 years ago
5
Genome browsing from MethylDackel bedGraphCpG file
#256
emiliomastriani
closed
1 year ago
1
Select only methylated CpG
#255
TSolDour
closed
2 years ago
5
Generating 5mCG per gene from BS/OXBS data
#254
hchetia
closed
2 years ago
3
More DMGs than DMRs
#253
TSolDour
closed
2 years ago
1
calculateDiffMeth
#252
DLGisch
closed
2 years ago
2
destranding in chunks can result in duplicate rows
#251
alexg9010
opened
2 years ago
0
Be more explicit about assocComp()$association meaning
#250
alexg9010
opened
2 years ago
0
How to obtained control and treatment %values instead of the diffmeth % value
#249
iramai
closed
2 years ago
4
When to use overdispersion adjustment for calculateDiffMeth
#248
kellyliyichen
closed
2 years ago
1
Accounting Covariates in my analysis
#247
priyatamapandey
closed
1 year ago
1
improve context validation
#246
alexg9010
opened
2 years ago
0
Error in vapply(object, function(x) x@context, FUN.VALUE = "character")
#245
hcph
closed
2 years ago
5
Converging multiple methylraw objects with 5hmc data into one
#244
hchetia
closed
2 years ago
9
What does this error imply?
#243
hchetia
closed
2 years ago
2
Error with creating methylkit object
#242
hchetia
closed
2 years ago
3
hg38 assembly
#241
hchetia
closed
2 years ago
1
How to use the function "adjustmethylC" effectively?
#240
hchetia
closed
2 years ago
4
Need advice on tiling the genome using computer with limited internal memory
#239
frylhc
closed
2 years ago
2
refseq.hg18.bed.txt and cpgi.hg18.bed.txt contains chr20, chr21, and chr22 only
#238
kbchoi
closed
2 years ago
1
methylation direction
#237
freedomq8
closed
2 years ago
1
Error in calculateDiffMeth for covariates with NAs
#236
TYRANISTAR
opened
2 years ago
1
Confusion about the algorithm of calculateDiffMeth when comparing multiple individuals from two groups
#235
HuangRuocheng
closed
2 years ago
2
Problem with unite() "Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL'"
#234
rhallPB
closed
3 years ago
2
Coerce dataframe into methylBase object
#233
laurahspencer
opened
3 years ago
1
Warning when unite gets only one methylraw object
#232
alexg9010
opened
3 years ago
1
Using ONT Megalodon bedmethyl files with methylkit
#231
fidibidi
closed
3 years ago
5
Simulator produces unrealistic beta values
#230
ashleymaeconard
closed
1 year ago
1
What does assocComp p-values suggest?
#229
geethavenk
closed
1 year ago
1
Error running methylkit with bismark output (genome wide cytosine report.txt)
#228
hchetia
closed
3 years ago
1
from % values to fold change
#227
iramai
closed
1 year ago
2
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