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Medips
•
reset
0
votes
0
replies
150
views
medips-output
ngsReports
MEDIPS
7 weeks ago
subhiksha
• 0
7
votes
18
replies
3.0k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 4 months ago by
Matthias Lienhard
▴ 240 • written 7.1 years ago by
justinburgener
▴ 20
0
votes
1
reply
282
views
MEDIPS - covariate
MEDIPS
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
James
• 0
0
votes
0
replies
300
views
CpG coverage with MEDIPS
MEDIPS
CpG
7 months ago
greta
• 0
0
votes
0
replies
536
views
How to use MeDIPS with BEDPE format input?
R
medip-seq
MEDIPS
15 months ago
Luomeng
• 0
1
vote
4
replies
1.1k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 19 months ago by
Simon Pearce
• 0 • written 19 months ago by
a.riediger
▴ 20
0
votes
2
replies
838
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 21 months ago by
Simon Pearce
• 0 • written 21 months ago by
Marianna
▴ 20
0
votes
2
replies
974
views
MEDIPS - error using MEDIPS.CpGenrich
MEDIPS
2.3 years ago • updated 2.2 years ago
Ian
• 0
0
votes
0
replies
742
views
MEDIPS.meth output
MEDIPS
edgeR
l
2.6 years ago
Aranzazu
• 0
0
votes
0
replies
677
views
MEDIPS - export wig with normalized counts
MEDIPS
3.2 years ago
lshepard
▴ 40
2
votes
4
replies
895
views
MEDIPS results differ with sample ordering
MEDIPS
edgeR
updated 4.0 years ago by
Lukas Chavez
▴ 570 • written 4.3 years ago by
keegan
▴ 60
2
votes
1
reply
815
views
MEDIPS - Error in MEDIPS.CpGenrich
MEDIPS
updated 4.1 years ago by
Lukas Chavez
▴ 570 • written 4.1 years ago by
gaurav4thareja
▴ 20
1
vote
1
reply
733
views
MEDIPS.CpGenrich now that RangedData is deprecated
MEDIPS
RangedData
GenomicRanges
updated 4.2 years ago by
Lukas Chavez
▴ 570 • written 4.2 years ago by
emham
• 0
1
vote
2
replies
959
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 4.2 years ago by
Matthias Lienhard
▴ 240 • written 4.2 years ago by
Simon Pearce
• 0
4
votes
5
replies
1.3k
views
Extracting normalized counts in MEDIPS
MEDIPS
MeDIP-seq
updated 2.6 years ago by
Lukas
▴ 20 • written 4.5 years ago by
lshepard
▴ 40
0
votes
0
replies
622
views
Why does MEDIPS only import read 1 when paired=TRUE for MEDIPS.createSet()function ?
#MEDIPS
MEDIPS
4.5 years ago
agm
• 0
1
vote
1
reply
878
views
sva correction for MEDIPS
MEDIPS
svaseq
sva
updated 5.3 years ago by
Lukas Chavez
▴ 570 • written 5.3 years ago by
tofukaj
• 0
0
votes
0
replies
981
views
error importing bam file for MEDIPS analysis
MEDIPS
bamfile
updated 5.3 years ago by
Bioconductor Community
0 • written 5.5 years ago by
oussama.badad
• 0
1
vote
2
replies
969
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.4 years ago by
Lukas Chavez
▴ 570 • written 5.4 years ago by
mtefit
• 0
0
votes
2
replies
1.1k
views
create.set on MEDIPS
medips
createset
updated 5.5 years ago by
Lukas Chavez
▴ 570 • written 5.5 years ago by
oussama.badad
• 0
0
votes
4
replies
1.2k
views
CpG density in MEDIPS
CpG
MEDIPS
5.6 years ago
saripalligautam86
▴ 10
0
votes
0
replies
990
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
5.6 years ago
saripalligautam86
▴ 10
0
votes
3
replies
1.1k
views
Coupling set error in MEDIPS
medips
coupling set error
cpg density
5.6 years ago
saripalligautam86
▴ 10
0
votes
0
replies
687
views
CouplingSet error in MeDIPS
MEDIPS
coupling set error
5.6 years ago
saripalligautam86
▴ 10
0
votes
3
replies
1.3k
views
MEDIPS - Annotation output explanation
MEDIPS
Output
6.0 years ago
vjain
• 0
1
vote
6
replies
1.9k
views
MEDIP: Problem with MEDIPS.createSet
medips
bsgenome
medip-seq
updated 6.1 years ago by
Lukas Chavez
▴ 570 • written 6.1 years ago by
vjain
• 0
3
votes
1
reply
1.2k
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 6.2 years ago by
Lukas Chavez
▴ 570 • written 6.2 years ago by
enrique.yeh
▴ 10
0
votes
6
replies
1.9k
views
MeDIPS: warning when using "ttest" settings in MEDIPS.meth
R
medips
medip-seq
7.7 years ago • updated 6.9 years ago
stb
• 0
3
votes
5
replies
1.6k
views
CNV parameter not working - MEDIPS
medips
medip-seq
error
lukas
updated 7.0 years ago by
Matthias Lienhard
▴ 240 • written 7.0 years ago by
anupriyaverma1408
• 0
1
vote
1
reply
1.2k
views
Window size for MEDIPS
medips
medip-seq
peak finding
luckas
updated 7.0 years ago by
Lukas Chavez
▴ 570 • written 7.0 years ago by
anupriyaverma1408
• 0
0
votes
2
replies
1.7k
views
MeQA and MEDIPS
bioconductor
meqa
medips
updated 7.0 years ago by
palchamy
• 0 • written 8.0 years ago by
manish.kumar
• 0
0
votes
1
reply
1.1k
views
How does the function MEDIPS.CpGenrich work?
medips
updated 7.0 years ago by
Lukas Chavez
▴ 570 • written 7.0 years ago by
stb
• 0
0
votes
1
reply
1.4k
views
Error raised during execution of MEDIPS package
medips
updated 7.1 years ago by
Lukas Chavez
▴ 570 • written 7.2 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 7.3 years ago by
Lukas Chavez
▴ 570 • written 7.3 years ago by
fmhsu0114
• 0
0
votes
1
reply
1.1k
views
Insertion size when using 'paired' in MEDIPS.createSet()
medips
R
medip-seq
pair-end reads
updated 7.4 years ago by
Lukas Chavez
▴ 570 • written 7.4 years ago by
stb
• 0
0
votes
1
reply
1.1k
views
How to make my custom genome available in MEDIPS?
MEDIPS
7.5 years ago
Vijay Lakhujani
• 0
0
votes
1
reply
1.3k
views
similar problem installing MEDIPS on Ubuntu 14.04
installation
medips
7.5 years ago
avilella
▴ 10
0
votes
1
reply
1.2k
views
MEDIPS - do reads without CG's get filtered out prior to analysis?
medips
updated 7.5 years ago by
Lukas Chavez
▴ 570 • written 7.6 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 7.6 years ago by
Lukas Chavez
▴ 570 • written 7.6 years ago by
stb
• 0
0
votes
1
reply
1.2k
views
Gene Symbol Annotation
medips
updated 7.7 years ago by
Lukas Chavez
▴ 570 • written 7.7 years ago by
peter.mcerlean
• 0
0
votes
1
reply
1.1k
views
TMM Normalization within MEDIPS ups some zero counts, is this normal?
MEDIPS
updated 7.7 years ago by
Lukas Chavez
▴ 570 • written 7.7 years ago by
jenniferlneary
• 0
1
vote
1
reply
1.5k
views
MeDIPS and use of the 'bwa' parameter
R
medip-seq
medips
bwa
updated 7.7 years ago by
Lukas Chavez
▴ 570 • written 7.7 years ago by
stb
• 0
1
vote
6
replies
1.4k
views
Alternative methylation contexts with MEDIPS?
MEDIPS
updated 7.8 years ago by
Matthias Lienhard
▴ 240 • written 7.8 years ago by
Chris Fields
▴ 90
0
votes
6
replies
1.6k
views
MEDIPS - input
MEDIPS
input
7.9 years ago
GFM
▴ 20
0
votes
1
reply
1.2k
views
Questions for MEDIPS getPairedGRange function in MEDIPS.readRegionsFile.R
medips
bam file
7.9 years ago
fkuo
▴ 10
0
votes
6
replies
2.0k
views
MEDIPS: Number of windows tested in Paired-end data set
medips
r
8.0 years ago
peter.mcerlean
• 0
0
votes
5
replies
1.6k
views
MEDIPS genome Vs createROIset significance issue
medips
r
8.2 years ago
peter.mcerlean
• 0
0
votes
1
reply
1.7k
views
Error in MEDIPS.calibrationCurve looking for different methylation profiles
medips
R
updated 8.2 years ago by
Lukas Chavez
▴ 570 • written 8.2 years ago by
pertille
• 0
0
votes
1
reply
1.3k
views
How to do FDR p.adj manually on "mr.edgeR object" from MEDIPS package?
R
Medips
edgeR
updated 8.2 years ago by
Lukas Chavez
▴ 570 • written 8.2 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 8.2 years ago by
Lukas Chavez
▴ 570 • written 8.2 years ago by
pertille
• 0
50 results • Page
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Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea()
by
James W. MacDonald
65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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