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ChIP-seq
•
reset
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
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
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq
chipqc
chip-seq
8.6 years ago
lindahove
▴ 10
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
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
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
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
5.7 years ago
94133
• 0
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
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
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
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind
ChIP-seq
updated 11 weeks ago by
Rory Stark
★ 5.1k • written 7.8 years ago by
xie186
• 0
1
vote
4
replies
883
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 4.5 years ago by
Theo
▴ 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
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw
chip-seq
clip-seq
9.2 years ago
IV
▴ 30
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
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
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
3
replies
841
views
normalization of ChIP-seq data
normalization
chip-seq
5.5 years ago
Bogdan
▴ 670
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 7.3 years ago by
siklenkak
• 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
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
0
votes
2
replies
1.9k
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
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
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 7.2 years ago by
Rory Stark
★ 5.1k • written 7.2 years ago by
siklenkak
• 0
3
votes
2
replies
888
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
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
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
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
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
0
votes
2
replies
1.1k
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
2
replies
915
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
0
votes
2
replies
1.2k
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
0
votes
1
reply
499
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
1
reply
710
views
meta-gene profiles
ChIP-seq
updated 2.1 years ago by
Guillaume Devailly
▴ 60 • written 2.1 years ago by
Bogdan
▴ 670
0
votes
1
reply
2.3k
views
diffBind - bam not accessible
diffbind
chip-seq
bam
8.5 years ago
eli7javasky
• 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
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
0
votes
1
reply
1.5k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi
chip-seq
region
updated 6.7 years ago by
Thomas Carroll
▴ 420 • written 6.7 years ago by
835102330
• 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
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
1
vote
1
reply
916
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
1
reply
818
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
2
votes
1
reply
991
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
▴ 40
2
votes
1
reply
925
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
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
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
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
0
replies
732
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Input Question for deseq.r
by
ATpoint
★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present
by
ATpoint
★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded
by
ATpoint
★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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