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Chip-Seq
•
reset
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
9.2 years ago
IV
▴ 30
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 7.5 years ago by
Aaron Lun
★ 28k • written 7.5 years ago by
s1437643
▴ 20
3
votes
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
8.6 years ago
lindahove
▴ 10
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
2
replies
890
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 7.2 years ago by
Wolfgang Huber
★ 13k • written 7.2 years ago by
Bogdan
▴ 670
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
siklenkak
• 0
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
16 months ago • updated 15 months ago
spg
• 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
5.8 years ago
94133
• 0
2
votes
1
reply
1.2k
views
problem with characters in chromosome names in DiffBind dba
DiffBind
ChIP-Seq
updated 9.4 years ago by
Rory Stark
★ 5.1k • written 9.4 years ago by
Georg Otto
▴ 120
2
votes
1
reply
996
views
How does csaw handle multiply aligned reads?
csaw
chip-seq
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
endrebak85
▴ 40
2
votes
2
replies
1.3k
views
How to use Diffbind as complete beginner?
diffbind
chip-seq
updated 6.8 years ago by
Gord Brown
▴ 650 • written 6.8 years ago by
AA
▴ 10
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 4.7 years ago by
zhenfeng.liu1
▴ 20 • written 5.2 years ago by
star
▴ 10
2
votes
1
reply
933
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
ATpoint
★ 4.0k
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq
diffBind
sequence_analysis
updated 3.8 years ago by
Rory Stark
★ 5.1k • written 3.8 years ago by
Mar Mar
▴ 20
1
vote
4
replies
886
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind
chip-seq
dba.peakset
updated 4.5 years ago by
Rory Stark
★ 5.1k • written 4.6 years ago by
Theo
▴ 10
1
vote
1
reply
823
views
Diffbind with age as blocking factor
diffbind
chip-seq
updated 4.5 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 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
jason.williams
• 0
1
vote
1
reply
922
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
1
vote
2
replies
1.6k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.6 years ago by
Hervé Pagès
16k • written 6.6 years ago by
gnani.science
• 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
6.4 years ago
chunhong.liu07
▴ 10
1
vote
5
replies
2.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind
dba.count
Chip-Seq
Differential analysis
updated 3.1 years ago by
Goku
• 0 • written 6.6 years ago by
urjaswita
▴ 40
1
vote
2
replies
923
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
21 months ago • updated 20 months ago
etiennedanis
• 0
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq
TSS
TMM
csaw
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
2.4k
views
diffBind - bam not accessible
diffbind
chip-seq
bam
8.5 years ago
eli7javasky
• 0
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 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
gil.hornung
• 0
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC
chip-seq
6.4 years ago
nbkingsley
• 0
0
votes
5
replies
1.4k
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 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
94133
• 0
0
votes
1
reply
1.3k
views
News:
Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course
RNA-Seq
Chip-seq
Parallel
News
9.1 years ago
Martin Morgan
25k
0
votes
7
replies
2.2k
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
0
votes
2
replies
1.0k
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
0
replies
905
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind
chip-seq
R
5.6 years ago
pierre.marin
• 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq
csaw
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Nicolas Servant
▴ 260
0
votes
3
replies
848
views
normalization of ChIP-seq data
normalization
chip-seq
5.5 years ago
Bogdan
▴ 670
0
votes
0
replies
872
views
Recommendation for visualizing ChIP-qPCR data?
R
chip-seq
histone chip-seq
ggbio
5.4 years ago
Ramiro Magno
▴ 100
0
votes
6
replies
1.7k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 12 months ago by
archibaldmarston
• 0 • written 23 months ago by
Bogdan
▴ 670
0
votes
1
reply
2.7k
views
Reading peaks from MACS2 with DiffBind
chip-seq
peak calling
diffbind
updated 4.9 years ago by
Rory Stark
★ 5.1k • written 4.9 years ago by
aviv.de-morgan
• 0
0
votes
0
replies
1.4k
views
Job:
Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing
RNA-Seq
ChIP-Seq
ATAC-Seq
Job
4.8 years ago • updated 4.7 years ago
Julie Zhu
★ 4.3k
0
votes
2
replies
1.2k
views
HOMER error: Where is the file?
HOMER
chip-seq
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
兆豪
• 0
0
votes
0
replies
735
views
Job:
Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq
ChIP-seq
Job
4.2 years ago
Johannes Rainer
★ 2.0k
0
votes
0
replies
687
views
ChIPQC cross-coverage plot
chipqc
chip-seq
4.0 years ago
tuteja.reetu
• 0
0
votes
1
reply
1.3k
views
use diffbind with normilized bedgraph files from spike ins
diffbind
chip-seq
chip
spike
spike-ins
updated 3.9 years ago by
Rory Stark
★ 5.1k • written 4.0 years ago by
Theo
▴ 10
0
votes
1
reply
502
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind
ChIP-seq
updated 3.9 years ago by
Rory Stark
★ 5.1k • written 3.9 years ago by
bioinfouser2
▴ 10
0
votes
2
replies
1.9k
views
Diffbind plotting on contrasts
diffbind
chip-seq
updated 8.2 years ago by
AB
▴ 110 • written 9.3 years ago by
medinaale
• 0
0
votes
2
replies
1.1k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind
MA plot
normalization
ChIP-seq
updated 3.8 years ago by
Rory Stark
★ 5.1k • written 3.8 years ago by
hasse.bossenbroek
• 0
0
votes
6
replies
1.8k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2
chip-seq
Differential binding
7.9 years ago
p2016k
• 0
0
votes
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 12 weeks ago by
Rory Stark
★ 5.1k • written 7.8 years ago by
xie186
• 0
0
votes
3
replies
4.0k
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 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
damian.kao
• 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
50 results • Page
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Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The U…
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swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
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65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
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I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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