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ChIP-seq
•
reset
3
votes
9
replies
2.8k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
8.6 years ago
lindahove
▴ 10
2
votes
7
replies
1.2k
views
Deferentially binding site is the same for all the samples
chip-seq
diffBind
sequence_analysis
updated 3.7 years ago by
Rory Stark
★ 5.1k • written 3.7 years ago by
Mar Mar
▴ 20
0
votes
7
replies
2.1k
views
Compute average score across multiple bed files
chip-seq
granges
R
bed files
updated 5.7 years ago by
spotifywebplayer
• 0 • written 5.7 years ago by
jinseok
• 0
1
vote
5
replies
2.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind
dba.count
Chip-Seq
Differential analysis
updated 3.0 years ago by
Goku
• 0 • written 6.5 years ago by
urjaswita
▴ 40
1
vote
2
replies
1.6k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.5 years ago by
Hervé Pagès
16k • written 6.5 years ago by
gnani.science
• 0
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 7.2 years ago by
Rory Stark
★ 5.1k • written 7.2 years ago by
siklenkak
• 0
0
votes
6
replies
1.8k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2
chip-seq
Differential binding
7.8 years ago
p2016k
• 0
1
vote
4
replies
869
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind
chip-seq
dba.peakset
updated 4.4 years ago by
Rory Stark
★ 5.1k • written 4.5 years ago by
Theo
• 0
0
votes
1
reply
1.0k
views
DiffBind: Different results with different chromosome names
diffbind
chip-seq
updated 7.6 years ago by
Rory Stark
★ 5.1k • written 7.6 years ago by
D.Hemerich
• 0
4
votes
2
replies
2.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
s1437643
▴ 20
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
siklenkak
• 0
0
votes
2
replies
1.6k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind
edger
deseq2
chip-seq
updated 7.1 years ago by
Rory Stark
★ 5.1k • written 7.2 years ago by
siklenkak
• 0
3
votes
2
replies
870
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 7.1 years ago by
Wolfgang Huber
★ 13k • written 7.1 years ago by
Bogdan
▴ 670
0
votes
1
reply
1.4k
views
Chip-seq peak annotation [Chipseeker]
chipseeker
chip-seq
annotation
Guangchuang
updated 6.8 years ago by
Guangchuang Yu
★ 1.2k • written 6.8 years ago by
anupriyaverma1408
• 0
2
votes
2
replies
1.3k
views
How to use Diffbind as complete beginner?
diffbind
chip-seq
updated 6.7 years ago by
Gord Brown
▴ 650 • written 6.7 years ago by
AA
▴ 10
0
votes
1
reply
1.4k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi
chip-seq
region
updated 6.6 years ago by
Thomas Carroll
▴ 420 • written 6.7 years ago by
835102330
• 0
3
votes
11
replies
2.3k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 6.7 years ago by
Ryan C. Thompson
★ 7.9k • written 6.7 years ago by
jms1223
▴ 10
3
votes
4
replies
1.5k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
15 months ago • updated 14 months ago
spg
• 0
0
votes
2
replies
1.8k
views
Diffbind plotting on contrasts
diffbind
chip-seq
updated 8.2 years ago by
AB
▴ 110 • written 9.2 years ago by
medinaale
• 0
4
votes
4
replies
1.5k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
9.1 years ago
IV
▴ 30
2
votes
1
reply
979
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
endrebak85
▴ 30
1
vote
18
replies
3.1k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
saadmurtazakhan
▴ 10
0
votes
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 9 weeks ago by
Rory Stark
★ 5.1k • written 7.7 years ago by
xie186
• 0
0
votes
3
replies
3.9k
views
DiffBind Analysis with more than 2 samples?
diffbind
chip-seq
updated 7.7 years ago by
Rory Stark
★ 5.1k • written 7.7 years ago by
sarah.blackstone7734
• 0
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq
differential binding analysis
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
damian.kao
• 0
0
votes
1
reply
2.6k
views
Reading peaks from MACS2 with DiffBind
chip-seq
peak calling
diffbind
updated 4.8 years ago by
Rory Stark
★ 5.1k • written 4.8 years ago by
aviv.de-morgan
• 0
1
vote
1
reply
801
views
Diffbind with age as blocking factor
diffbind
chip-seq
updated 4.4 years ago by
Rory Stark
★ 5.1k • written 4.5 years ago by
melnuesch
▴ 10
1
vote
4
replies
1.3k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR
RNA-seq
ChIP-seq
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
jason.williams
• 0
2
votes
1
reply
905
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
ATpoint
★ 4.0k
0
votes
1
reply
1.3k
views
use diffbind with normilized bedgraph files from spike ins
diffbind
chip-seq
chip
spike
spike-ins
updated 3.8 years ago by
Rory Stark
★ 5.1k • written 3.9 years ago by
Theo
• 0
0
votes
1
reply
490
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind
ChIP-seq
updated 3.8 years ago by
Rory Stark
★ 5.1k • written 3.9 years ago by
bioinfouser2
▴ 10
0
votes
2
replies
1.0k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind
MA plot
normalization
ChIP-seq
updated 3.7 years ago by
Rory Stark
★ 5.1k • written 3.7 years ago by
hasse.bossenbroek
• 0
1
vote
1
reply
899
views
Error in dba.count and dba.analyze
DiffBind
chip-seq
differentially-binding-site
updated 3.5 years ago by
Rory Stark
★ 5.1k • written 3.5 years ago by
Mar Mar
▴ 20
0
votes
1
reply
692
views
meta-gene profiles
ChIP-seq
updated 2.1 years ago by
Guillaume Devailly
▴ 60 • written 2.1 years ago by
Bogdan
▴ 670
1
vote
2
replies
882
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
20 months ago
etiennedanis
• 0
0
votes
6
replies
1.6k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 11 months ago by
archibaldmarston
• 0 • written 22 months ago by
Bogdan
▴ 670
0
votes
2
replies
1.1k
views
HOMER error: Where is the file?
HOMER
chip-seq
updated 17 months ago by
ATpoint
★ 4.0k • written 17 months ago by
兆豪
• 0
2
votes
1
reply
1.2k
views
problem with characters in chromosome names in DiffBind dba
DiffBind
ChIP-Seq
updated 9.3 years ago by
Rory Stark
★ 5.1k • written 9.3 years ago by
Georg Otto
▴ 120
0
votes
2
replies
1.2k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw
histone chip-seq
chip-seq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
gil.hornung
• 0
1
vote
1
reply
2.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind
macs2
chip-seq
6.3 years ago
chunhong.liu07
▴ 10
0
votes
5
replies
1.3k
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 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
94133
• 0
0
votes
2
replies
993
views
csaw normalization and library size
chip-seq
normalization
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Nicolas Servant
▴ 260
0
votes
4
replies
1.3k
views
csaw spike-in normalization
ChIP-seq
csaw
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
Nicolas Servant
▴ 260
2
votes
2
replies
1.2k
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation
affymetrix microarrays
chip-seq
affymetrix mouse gene arrays
5.4 years ago
2323982403
▴ 60
2
votes
2
replies
1.3k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq
ChIPQC
QC
updated 4.6 years ago by
zhenfeng.liu1
▴ 20 • written 5.1 years ago by
star
▴ 10
0
votes
0
replies
830
views
Meta-Analysis chip-seq data
chip-seq
meta-analysis
6.8 years ago
rezapanahi222
• 0
0
votes
0
replies
959
views
Job:
Post-doctoral position in algorithms for cancer data analysis
algorithms
ChIP-seq
cancer
Job
7.8 years ago
valentina.boeva
• 0
0
votes
0
replies
853
views
Recommendation for visualizing ChIP-qPCR data?
R
chip-seq
histone chip-seq
ggbio
5.3 years ago
Ramiro Magno
▴ 100
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC
chip-seq
6.3 years ago
nbkingsley
• 0
0
votes
0
replies
670
views
ChIPQC cross-coverage plot
chipqc
chip-seq
4.0 years ago
tuteja.reetu
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
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41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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