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ChIP-seq
•
reset
0
votes
4
replies
126
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 2 days ago by
ATpoint
★ 1.2k • written 5 days ago by
Bogdan
▴ 640
0
votes
1
reply
121
views
meta-gene profiles
ChIP-seq
updated 11 weeks ago by
Guillaume Devailly
▴ 40 • written 11 weeks ago by
Bogdan
▴ 640
1
vote
1
reply
367
views
Error in dba.count and dba.analyze
DiffBind
chip-seq
differentially-binding-site
updated 19 months ago by
Rory Stark
★ 4.4k • written 19 months ago by
Mar Mar
▴ 20
0
votes
2
replies
378
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind
MA plot
normalization
ChIP-seq
updated 22 months ago by
Rory Stark
★ 4.4k • written 22 months ago by
hasse.bossenbroek
• 0
2
votes
7
replies
608
views
Deferentially binding site is the same for all the samples
chip-seq
diffBind
sequence_analysis
updated 22 months ago by
Rory Stark
★ 4.4k • written 22 months ago by
Mar Mar
▴ 20
0
votes
1
reply
200
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind
ChIP-seq
updated 23 months ago by
Rory Stark
★ 4.4k • written 2.0 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
352
views
use diffbind with normilized bedgraph files from spike ins
diffbind
chip-seq
chip
spike
spike-ins
updated 23 months ago by
Rory Stark
★ 4.4k • written 2.1 years ago by
theodore.georgomanolis
• 0
0
votes
0
replies
262
views
ChIPQC cross-coverage plot
chipqc
chip-seq
2.1 years ago
tuteja.reetu
• 0
0
votes
0
replies
267
views
Job:
Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq
ChIP-seq
Job
2.3 years ago
Johannes Rainer
★ 1.9k
2
votes
1
reply
350
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 2.4 years ago by
Aaron Lun
★ 27k • written 2.4 years ago by
ATpoint
★ 1.2k
1
vote
4
replies
612
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR
RNA-seq
ChIP-seq
updated 2.6 years ago by
James W. MacDonald
59k • written 2.6 years ago by
jason.williams
• 0
1
vote
4
replies
352
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind
chip-seq
dba.peakset
updated 2.6 years ago by
Rory Stark
★ 4.4k • written 2.6 years ago by
theodore.georgomanolis
• 0
1
vote
1
reply
370
views
Diffbind with age as blocking factor
diffbind
chip-seq
updated 2.6 years ago by
Rory Stark
★ 4.4k • written 2.6 years ago by
melnuesch
▴ 10
0
votes
0
replies
1.0k
views
Job:
Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing
RNA-Seq
ChIP-Seq
ATAC-Seq
Job
2.9 years ago • updated 2.8 years ago
Julie Zhu
★ 4.3k
2
votes
2
replies
809
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq
ChIPQC
QC
updated 2.8 years ago by
zhenfeng.liu1
▴ 20 • written 3.3 years ago by
star
▴ 10
0
votes
1
reply
1.2k
views
Reading peaks from MACS2 with DiffBind
chip-seq
peak calling
diffbind
updated 3.0 years ago by
Rory Stark
★ 4.4k • written 3.0 years ago by
aviv.de-morgan
• 0
0
votes
0
replies
469
views
Recommendation for visualizing ChIP-qPCR data?
R
chip-seq
histone chip-seq
ggbio
3.4 years ago
Ramiro Magno
▴ 100
2
votes
2
replies
599
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation
affymetrix microarrays
chip-seq
affymetrix mouse gene arrays
3.5 years ago
2323982403
▴ 50
0
votes
3
replies
420
views
normalization of ChIP-seq data
normalization
chip-seq
3.5 years ago
Bogdan
▴ 640
0
votes
4
replies
677
views
csaw spike-in normalization
ChIP-seq
csaw
updated 3.6 years ago by
Aaron Lun
★ 27k • written 3.6 years ago by
Nicolas Servant
▴ 260
0
votes
0
replies
476
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind
chip-seq
R
3.6 years ago
pierre.marin
• 0
0
votes
2
replies
521
views
csaw normalization and library size
chip-seq
normalization
updated 3.8 years ago by
Aaron Lun
★ 27k • written 3.8 years ago by
Nicolas Servant
▴ 260
0
votes
7
replies
1.1k
views
Compute average score across multiple bed files
chip-seq
granges
R
bed files
updated 3.8 years ago by
spotifywebplayer
• 0 • written 3.8 years ago by
jinseok
• 0
3
votes
6
replies
840
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
3.8 years ago
94133
• 0
0
votes
5
replies
747
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 4.0 years ago by
Aaron Lun
★ 27k • written 4.0 years ago by
94133
• 0
1
vote
1
reply
1.5k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind
macs2
chip-seq
4.5 years ago
chunhong.liu07
▴ 10
0
votes
0
replies
753
views
ChIPQC: Error in names(res) <- nms
ChIPQC
chip-seq
4.5 years ago
nbkingsley
• 0
1
vote
5
replies
1.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind
dba.count
Chip-Seq
Differential analysis
updated 14 months ago by
Goku
• 0 • written 4.7 years ago by
urjaswita
▴ 40
0
votes
2
replies
723
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw
histone chip-seq
chip-seq
updated 4.7 years ago by
Aaron Lun
★ 27k • written 4.7 years ago by
gil.hornung
• 0
1
vote
2
replies
868
views
Errors with makeTxDbFromBiomart
chip-seq
updated 4.7 years ago by
Hervé Pagès
15k • written 4.7 years ago by
gnani.science
• 0
0
votes
1
reply
976
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi
chip-seq
region
updated 4.8 years ago by
Thomas Carroll
▴ 400 • written 4.8 years ago by
835102330
• 0
2
votes
11
replies
1.5k
views
Exporting normalized counts over final DB windows from csaw
csaw
edger
chip-seq
updated 4.8 years ago by
Ryan C. Thompson
7.8k • written 4.8 years ago by
jms1223
• 0
2
votes
2
replies
806
views
How to use Diffbind as complete beginner?
diffbind
chip-seq
updated 4.9 years ago by
Gord Brown
▴ 640 • written 4.9 years ago by
AA
▴ 10
0
votes
1
reply
984
views
Chip-seq peak annotation [Chipseeker]
chipseeker
chip-seq
annotation
Guangchuang
updated 4.9 years ago by
Guangchuang Yu
★ 1.2k • written 4.9 years ago by
anupriyaverma1408
• 0
0
votes
0
replies
583
views
Meta-Analysis chip-seq data
chip-seq
meta-analysis
5.0 years ago
rezapanahi222
• 0
3
votes
2
replies
563
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 5.2 years ago by
Wolfgang Huber
13k • written 5.2 years ago by
Bogdan
▴ 640
0
votes
2
replies
1.1k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind
edger
deseq2
chip-seq
updated 5.3 years ago by
Rory Stark
★ 4.4k • written 5.3 years ago by
siklenkak
• 0
0
votes
3
replies
1.3k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind
chip-seq
normalization
deseq2
tmm
updated 5.3 years ago by
Rory Stark
★ 4.4k • written 5.4 years ago by
siklenkak
• 0
3
votes
4
replies
1.2k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 5.4 years ago by
Aaron Lun
★ 27k • written 5.4 years ago by
siklenkak
• 0
3
votes
2
replies
1.4k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw
chip-seq
normalization
edger
cqn
updated 5.6 years ago by
Aaron Lun
★ 27k • written 5.6 years ago by
s1437643
▴ 10
0
votes
1
reply
678
views
DiffBind: Different results with different chromosome names
diffbind
chip-seq
updated 5.7 years ago by
Rory Stark
★ 4.4k • written 5.7 years ago by
D.Hemerich
• 0
0
votes
3
replies
810
views
Chip-seq analysis with input
chip-seq
differential binding analysis
updated 5.8 years ago by
Aaron Lun
★ 27k • written 5.8 years ago by
damian.kao
• 0
0
votes
3
replies
2.9k
views
DiffBind Analysis with more than 2 samples?
diffbind
chip-seq
updated 5.8 years ago by
Rory Stark
★ 4.4k • written 5.8 years ago by
sarah.blackstone7734
• 0
0
votes
2
replies
1.1k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 5.9 years ago by
Rory Stark
★ 4.4k • written 5.9 years ago by
xie186
• 0
0
votes
6
replies
1.3k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2
chip-seq
Differential binding
6.0 years ago
p2016k
• 0
1
vote
18
replies
2.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 6.0 years ago by
Aaron Lun
★ 27k • written 6.0 years ago by
saadmurtazakhan
▴ 10
0
votes
0
replies
699
views
Job:
Post-doctoral position in algorithms for cancer data analysis
algorithms
ChIP-seq
cancer
Job
6.0 years ago
valentina.boeva
• 0
2
votes
1
reply
707
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 6.0 years ago by
Aaron Lun
★ 27k • written 6.0 years ago by
endrebak85
▴ 30
0
votes
0
replies
868
views
Job:
Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing
rna-seq
chip-seq
single cell
Job
6.1 years ago
Katja Hebestreit
▴ 130
0
votes
2
replies
1.4k
views
Diffbind plotting on contrasts
diffbind
chip-seq
updated 6.3 years ago by
AB
▴ 100 • written 7.3 years ago by
medinaale
• 0
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