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ChIP-seq
•
reset
3
votes
9
replies
2.2k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
7.4 years ago
lindahove
▴ 10
2
votes
7
replies
769
views
Deferentially binding site is the same for all the samples
chip-seq
diffBind
sequence_analysis
updated 2.5 years ago by
Rory Stark
★ 4.6k • written 2.5 years ago by
Mar Mar
▴ 20
0
votes
7
replies
1.3k
views
Compute average score across multiple bed files
chip-seq
granges
R
bed files
updated 4.5 years ago by
spotifywebplayer
• 0 • written 4.5 years ago by
jinseok
• 0
1
vote
5
replies
1.7k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind
dba.count
Chip-Seq
Differential analysis
updated 22 months ago by
Goku
• 0 • written 5.4 years ago by
urjaswita
▴ 40
1
vote
2
replies
1.0k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 5.4 years ago by
Hervé Pagès
16k • written 5.4 years ago by
gnani.science
• 0
0
votes
3
replies
1.5k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 6.0 years ago by
Rory Stark
★ 4.6k • written 6.0 years ago by
siklenkak
• 0
0
votes
6
replies
1.4k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2
chip-seq
Differential binding
6.6 years ago
p2016k
• 0
1
vote
4
replies
484
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind
chip-seq
dba.peakset
updated 3.3 years ago by
Rory Stark
★ 4.6k • written 3.3 years ago by
theodore.georgomanolis
• 0
0
votes
1
reply
761
views
DiffBind: Different results with different chromosome names
diffbind
chip-seq
updated 6.4 years ago by
Rory Stark
★ 4.6k • written 6.4 years ago by
D.Hemerich
• 0
3
votes
2
replies
1.6k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
s1437643
▴ 10
3
votes
4
replies
1.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
siklenkak
• 0
0
votes
2
replies
1.2k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind
edger
deseq2
chip-seq
updated 6.0 years ago by
Rory Stark
★ 4.6k • written 6.0 years ago by
siklenkak
• 0
3
votes
2
replies
643
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 5.9 years ago by
Wolfgang Huber
13k • written 5.9 years ago by
Bogdan
▴ 660
0
votes
1
reply
1.1k
views
Chip-seq peak annotation [Chipseeker]
chipseeker
chip-seq
annotation
Guangchuang
updated 5.6 years ago by
Guangchuang Yu
★ 1.2k • written 5.6 years ago by
anupriyaverma1408
• 0
2
votes
2
replies
939
views
How to use Diffbind as complete beginner?
diffbind
chip-seq
updated 5.5 years ago by
Gord Brown
▴ 650 • written 5.5 years ago by
AA
▴ 10
0
votes
1
reply
1.1k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi
chip-seq
region
updated 5.4 years ago by
Thomas Carroll
▴ 420 • written 5.5 years ago by
835102330
• 0
3
votes
11
replies
1.7k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 5.5 years ago by
Ryan C. Thompson
7.8k • written 5.5 years ago by
jms1223
▴ 10
3
votes
4
replies
296
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
6 weeks ago • updated 20 days ago
spg
• 0
0
votes
2
replies
1.5k
views
Diffbind plotting on contrasts
diffbind
chip-seq
updated 7.0 years ago by
AB
▴ 110 • written 8.0 years ago by
medinaale
• 0
4
votes
4
replies
1.2k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
8.0 years ago
IV
▴ 30
2
votes
1
reply
774
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
endrebak85
▴ 30
1
vote
18
replies
2.4k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
saadmurtazakhan
▴ 10
0
votes
2
replies
1.3k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 6.6 years ago by
Rory Stark
★ 4.6k • written 6.6 years ago by
xie186
• 0
0
votes
3
replies
3.2k
views
DiffBind Analysis with more than 2 samples?
diffbind
chip-seq
updated 6.5 years ago by
Rory Stark
★ 4.6k • written 6.5 years ago by
sarah.blackstone7734
• 0
0
votes
3
replies
914
views
Chip-seq analysis with input
chip-seq
differential binding analysis
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
damian.kao
• 0
0
votes
1
reply
1.6k
views
Reading peaks from MACS2 with DiffBind
chip-seq
peak calling
diffbind
updated 3.7 years ago by
Rory Stark
★ 4.6k • written 3.7 years ago by
aviv.de-morgan
• 0
1
vote
1
reply
481
views
Diffbind with age as blocking factor
diffbind
chip-seq
updated 3.3 years ago by
Rory Stark
★ 4.6k • written 3.3 years ago by
melnuesch
▴ 10
1
vote
4
replies
836
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR
RNA-seq
ChIP-seq
updated 3.2 years ago by
James W. MacDonald
62k • written 3.2 years ago by
jason.williams
• 0
2
votes
1
reply
495
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
ATpoint
★ 2.1k
0
votes
1
reply
638
views
use diffbind with normilized bedgraph files from spike ins
diffbind
chip-seq
chip
spike
spike-ins
updated 2.6 years ago by
Rory Stark
★ 4.6k • written 2.7 years ago by
theodore.georgomanolis
• 0
0
votes
1
reply
281
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind
ChIP-seq
updated 2.6 years ago by
Rory Stark
★ 4.6k • written 2.7 years ago by
bioinfouser2
▴ 10
0
votes
2
replies
581
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind
MA plot
normalization
ChIP-seq
updated 2.5 years ago by
Rory Stark
★ 4.6k • written 2.5 years ago by
hasse.bossenbroek
• 0
1
vote
1
reply
536
views
Error in dba.count and dba.analyze
DiffBind
chip-seq
differentially-binding-site
updated 2.3 years ago by
Rory Stark
★ 4.6k • written 2.3 years ago by
Mar Mar
▴ 20
0
votes
1
reply
318
views
meta-gene profiles
ChIP-seq
updated 11 months ago by
Guillaume Devailly
▴ 60 • written 11 months ago by
Bogdan
▴ 660
1
vote
2
replies
316
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
6 months ago • updated 5 months ago
etiennedanis
• 0
0
votes
5
replies
568
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 7 months ago by
etiennedanis
• 0 • written 8 months ago by
Bogdan
▴ 660
0
votes
2
replies
228
views
HOMER error: Where is the file?
HOMER
chip-seq
updated 12 weeks ago by
ATpoint
★ 2.1k • written 12 weeks ago by
兆豪
• 0
2
votes
1
reply
989
views
problem with characters in chromosome names in DiffBind dba
DiffBind
ChIP-Seq
updated 8.2 years ago by
Rory Stark
★ 4.6k • written 8.2 years ago by
Georg Otto
▴ 120
0
votes
2
replies
843
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw
histone chip-seq
chip-seq
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
gil.hornung
• 0
1
vote
1
reply
1.7k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind
macs2
chip-seq
5.1 years ago
chunhong.liu07
▴ 10
0
votes
5
replies
869
views
CSAW Spike In Normalization: Error in .local(object, ...) : library sizes of 'se.out' and 'object' are not identical
csaw
software error
R
chip-seq
bioconductor
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
94133
• 0
0
votes
2
replies
627
views
csaw normalization and library size
chip-seq
normalization
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
Nicolas Servant
▴ 260
0
votes
4
replies
823
views
csaw spike-in normalization
ChIP-seq
csaw
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Nicolas Servant
▴ 260
2
votes
2
replies
739
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation
affymetrix microarrays
chip-seq
affymetrix mouse gene arrays
4.2 years ago
2323982403
▴ 50
2
votes
2
replies
947
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq
ChIPQC
QC
updated 3.5 years ago by
zhenfeng.liu1
▴ 20 • written 3.9 years ago by
star
▴ 10
0
votes
0
replies
659
views
Meta-Analysis chip-seq data
chip-seq
meta-analysis
5.6 years ago
rezapanahi222
• 0
0
votes
0
replies
767
views
Job:
Post-doctoral position in algorithms for cancer data analysis
algorithms
ChIP-seq
cancer
Job
6.7 years ago
valentina.boeva
• 0
0
votes
0
replies
590
views
Recommendation for visualizing ChIP-qPCR data?
R
chip-seq
histone chip-seq
ggbio
4.1 years ago
Ramiro Magno
▴ 100
0
votes
0
replies
850
views
ChIPQC: Error in names(res) <- nms
ChIPQC
chip-seq
5.2 years ago
nbkingsley
• 0
0
votes
0
replies
390
views
ChIPQC cross-coverage plot
chipqc
chip-seq
2.8 years ago
tuteja.reetu
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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