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medips
•
reset
0
votes
0
replies
234
views
medips-output
ngsReports
MEDIPS
4 months ago
Researcher
• 0
7
votes
18
replies
3.2k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 6 months ago by
Matthias Lienhard
▴ 240 • written 7.3 years ago by
justinburgener
▴ 20
0
votes
1
reply
344
views
MEDIPS - covariate
MEDIPS
updated 9 months ago by
James W. MacDonald
66k • written 9 months ago by
James
• 0
0
votes
0
replies
351
views
CpG coverage with MEDIPS
MEDIPS
CpG
10 months ago
greta
• 0
0
votes
0
replies
606
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
17 months ago
Luomeng
• 0
1
vote
4
replies
1.2k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 22 months ago by
Simon Pearce
• 0 • written 22 months ago by
a.riediger
▴ 20
0
votes
2
replies
917
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 23 months ago by
Simon Pearce
• 0 • written 24 months ago by
Marianna
▴ 20
0
votes
2
replies
1.1k
views
MEDIPS - error using MEDIPS.CpGenrich
MEDIPS
2.5 years ago
Ian
• 0
0
votes
0
replies
791
views
MEDIPS.meth output
MEDIPS
edgeR
l
2.9 years ago
Aranzazu
• 0
0
votes
0
replies
718
views
MEDIPS - export wig with normalized counts
MEDIPS
3.4 years ago
lshepard
▴ 40
2
votes
4
replies
970
views
MEDIPS results differ with sample ordering
MEDIPS
edgeR
updated 4.2 years ago by
Lukas Chavez
▴ 570 • written 4.5 years ago by
keegan
▴ 60
2
votes
1
reply
867
views
MEDIPS - Error in MEDIPS.CpGenrich
MEDIPS
updated 4.4 years ago by
Lukas Chavez
▴ 570 • written 4.4 years ago by
gaurav4thareja
▴ 20
1
vote
1
reply
782
views
MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS
RangedData
GenomicRanges
updated 4.4 years ago by
Lukas Chavez
▴ 570 • written 4.4 years ago by
emham
• 0
1
vote
2
replies
1.1k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 4.4 years ago by
Matthias Lienhard
▴ 240 • written 4.4 years ago by
Simon Pearce
• 0
4
votes
5
replies
1.4k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 2.8 years ago by
Lukas
▴ 20 • written 4.7 years ago by
lshepard
▴ 40
0
votes
0
replies
688
views
Why does MEDIPS only import read 1 when paired=TRUE for MEDIPS.createSet()function ?
#MEDIPS
MEDIPS
4.7 years ago
agm
• 0
1
vote
1
reply
937
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 5.5 years ago by
Lukas Chavez
▴ 570 • written 5.5 years ago by
tofukaj
• 0
0
votes
0
replies
1.0k
views
error importing bam file for MEDIPS analysis
MEDIPS
bamfile
updated 5.5 years ago by
Bioconductor Community
0 • written 5.7 years ago by
oussama.badad
• 0
1
vote
2
replies
1.0k
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.7 years ago by
Lukas Chavez
▴ 570 • written 5.7 years ago by
mtefit
• 0
0
votes
2
replies
1.2k
views
create.set on MEDIPS
medips
createset
updated 5.7 years ago by
Lukas Chavez
▴ 570 • written 5.7 years ago by
oussama.badad
• 0
0
votes
4
replies
1.3k
views
CpG density in MEDIPS
CpG
MEDIPS
5.8 years ago
saripalligautam86
▴ 10
0
votes
0
replies
1.1k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
5.8 years ago
saripalligautam86
▴ 10
0
votes
3
replies
1.1k
views
Coupling set error in MEDIPS
medips
coupling set error
cpg density
5.8 years ago
saripalligautam86
▴ 10
0
votes
0
replies
731
views
CouplingSet error in MeDIPS
MEDIPS
coupling set error
5.8 years ago
saripalligautam86
▴ 10
0
votes
3
replies
1.4k
views
MEDIPS - Annotation output explanation
MEDIPS
Output
6.2 years ago
vjain
• 0
1
vote
6
replies
2.0k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 6.4 years ago by
Lukas Chavez
▴ 570 • written 6.4 years ago by
vjain
• 0
3
votes
1
reply
1.2k
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 6.4 years ago by
Lukas Chavez
▴ 570 • written 6.4 years ago by
enrique.yeh
▴ 10
0
votes
6
replies
2.0k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R
medips
medip-seq
8.0 years ago • updated 7.1 years ago
stb
• 0
3
votes
5
replies
1.7k
views
CNV parameter not working - MEDIPS
medips
medip-seq
error
lukas
updated 7.2 years ago by
Matthias Lienhard
▴ 240 • written 7.2 years ago by
anupriyaverma1408
• 0
1
vote
1
reply
1.3k
views
Window size for MEDIPS
medips
medip-seq
peak finding
luckas
updated 7.2 years ago by
Lukas Chavez
▴ 570 • written 7.2 years ago by
anupriyaverma1408
• 0
0
votes
2
replies
1.8k
views
MeQA and MEDIPS
bioconductor
meqa
medips
updated 7.2 years ago by
palchamy
• 0 • written 8.2 years ago by
manish.kumar
• 0
0
votes
1
reply
1.1k
views
How does the function MEDIPS.CpGenrich work?
medips
updated 7.3 years ago by
Lukas Chavez
▴ 570 • written 7.3 years ago by
stb
• 0
0
votes
1
reply
1.5k
views
Error raised during execution of MEDIPS package
medips
updated 7.4 years ago by
Lukas Chavez
▴ 570 • written 7.4 years ago by
pinky_pinkpinky
• 0
0
votes
1
reply
1.1k
views
MEDIPS: case study with different replicate numbers of control and case
MEDIPS
updated 7.5 years ago by
Lukas Chavez
▴ 570 • written 7.5 years ago by
fmhsu0114
• 0
0
votes
1
reply
1.2k
views
Insertion size when using 'paired' in MEDIPS.createSet()
medips
R
medip-seq
pair-end reads
updated 7.6 years ago by
Lukas Chavez
▴ 570 • written 7.6 years ago by
stb
• 0
0
votes
1
reply
1.1k
views
How to make my custom genome available in MEDIPS?
MEDIPS
7.7 years ago
Vijay Lakhujani
• 0
0
votes
1
reply
1.4k
views
similar problem installing MEDIPS on Ubuntu 14.04
installation
medips
7.8 years ago • updated 7.7 years ago
avilella
▴ 10
0
votes
1
reply
1.3k
views
MEDIPS - do reads without CG's get filtered out prior to analysis?
medips
updated 7.8 years ago by
Lukas Chavez
▴ 570 • written 7.8 years ago by
chu_shirley
• 0
0
votes
1
reply
1.1k
views
How does the 'paired' argument works in MeDIPS 1.23.2
medips
medip-seq
R
pair-end reads
updated 7.8 years ago by
Lukas Chavez
▴ 570 • written 7.8 years ago by
stb
• 0
0
votes
1
reply
1.2k
views
Gene Symbol Annotation
medips
updated 7.9 years ago by
Lukas Chavez
▴ 570 • written 7.9 years ago by
peter.mcerlean
• 0
0
votes
1
reply
1.2k
views
TMM Normalization within MEDIPS ups some zero counts, is this normal?
MEDIPS
updated 8.0 years ago by
Lukas Chavez
▴ 570 • written 8.0 years ago by
jenniferlneary
• 0
1
vote
1
reply
1.6k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 8.0 years ago by
Lukas Chavez
▴ 570 • written 8.0 years ago by
stb
• 0
1
vote
6
replies
1.5k
views
Alternative methylation contexts with MEDIPS?
MEDIPS
updated 8.0 years ago by
Matthias Lienhard
▴ 240 • written 8.0 years ago by
Chris Fields
▴ 90
0
votes
6
replies
1.7k
views
MEDIPS - input
MEDIPS
input
8.1 years ago
GFM
▴ 20
0
votes
1
reply
1.3k
views
Questions for MEDIPS getPairedGRange function in MEDIPS.readRegionsFile.R
medips
bam file
8.1 years ago
fkuo
▴ 10
0
votes
6
replies
2.1k
views
MEDIPS: Number of windows tested in Paired-end data set
medips
r
8.3 years ago
peter.mcerlean
• 0
0
votes
5
replies
1.7k
views
MEDIPS genome Vs createROIset significance issue
medips
r
8.4 years ago
peter.mcerlean
• 0
0
votes
1
reply
1.7k
views
Error in MEDIPS.calibrationCurve looking for different methylation profiles
medips
R
updated 8.5 years ago by
Lukas Chavez
▴ 570 • written 8.5 years ago by
pertille
• 0
0
votes
1
reply
1.4k
views
How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
R
Medips
edgeR
updated 8.5 years ago by
Lukas Chavez
▴ 570 • written 8.5 years ago by
pertille
• 0
2
votes
1
reply
1.2k
views
How createSet from reduced "paire-ed" sequencing on MeDIPS?
medips
R
input files
updated 8.5 years ago by
Lukas Chavez
▴ 570 • written 8.5 years ago by
pertille
• 0
50 results • Page
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Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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