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ChIP-seq
•
reset
3
votes
4
replies
315
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind
SpikeIn
Normalization
ChIP-seq
csaw
7 weeks ago • updated 28 days ago
spg
• 0
0
votes
2
replies
253
views
HOMER error: Where is the file?
HOMER
chip-seq
updated 3 months ago by
ATpoint
★ 2.1k • written 3 months ago by
兆豪
• 0
1
vote
2
replies
323
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
6 months ago
etiennedanis
• 0
0
votes
5
replies
584
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
1
reply
325
views
meta-gene profiles
ChIP-seq
updated 11 months ago by
Guillaume Devailly
▴ 60 • written 11 months ago by
Bogdan
▴ 660
1
vote
1
reply
541
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
2
replies
587
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
2
votes
7
replies
776
views
Deferentially binding site is the same for all the samples
chip-seq
diffBind
sequence_analysis
updated 2.6 years ago by
Rory Stark
★ 4.6k • written 2.6 years ago by
Mar Mar
▴ 20
0
votes
1
reply
284
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind
ChIP-seq
updated 2.7 years ago by
Rory Stark
★ 4.6k • written 2.7 years ago by
bioinfouser2
▴ 10
0
votes
1
reply
672
views
use diffbind with normilized bedgraph files from spike ins
diffbind
chip-seq
chip
spike
spike-ins
updated 2.7 years ago by
Rory Stark
★ 4.6k • written 2.8 years ago by
theodore.georgomanolis
• 0
0
votes
0
replies
396
views
ChIPQC cross-coverage plot
chipqc
chip-seq
2.8 years ago
tuteja.reetu
• 0
0
votes
0
replies
390
views
Job:
Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq
ChIP-seq
Job
3.0 years ago
Johannes Rainer
★ 2.0k
2
votes
1
reply
499
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
1
vote
4
replies
849
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR
RNA-seq
ChIP-seq
updated 3.3 years ago by
James W. MacDonald
62k • written 3.3 years ago by
jason.williams
• 0
1
vote
4
replies
489
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
1
vote
1
reply
485
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
0
votes
0
replies
1.1k
views
Job:
Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing
RNA-Seq
ChIP-Seq
ATAC-Seq
Job
3.6 years ago • updated 3.5 years ago
Julie Zhu
★ 4.3k
2
votes
2
replies
952
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 4.0 years ago by
star
▴ 10
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
0
votes
0
replies
592
views
Recommendation for visualizing ChIP-qPCR data?
R
chip-seq
histone chip-seq
ggbio
4.1 years ago
Ramiro Magno
▴ 100
2
votes
2
replies
744
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
0
votes
3
replies
545
views
normalization of ChIP-seq data
normalization
chip-seq
4.2 years ago
Bogdan
▴ 660
0
votes
4
replies
833
views
csaw spike-in normalization
ChIP-seq
csaw
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
Nicolas Servant
▴ 260
0
votes
0
replies
569
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind
chip-seq
R
4.3 years ago
pierre.marin
• 0
0
votes
2
replies
629
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
7
replies
1.4k
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
3
votes
6
replies
997
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq
chippeakanno
chipseeker
4.5 years ago
94133
• 0
0
votes
5
replies
871
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
1
vote
1
reply
1.7k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind
macs2
chip-seq
5.2 years ago
chunhong.liu07
▴ 10
0
votes
0
replies
854
views
ChIPQC: Error in names(res) <- nms
ChIPQC
chip-seq
5.2 years ago
nbkingsley
• 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
0
votes
2
replies
845
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
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
1
reply
1.1k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi
chip-seq
region
updated 5.5 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
2
votes
2
replies
945
views
How to use Diffbind as complete beginner?
diffbind
chip-seq
updated 5.6 years ago by
Gord Brown
▴ 650 • written 5.6 years ago by
AA
▴ 10
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
0
votes
0
replies
670
views
Meta-Analysis chip-seq data
chip-seq
meta-analysis
5.7 years ago
rezapanahi222
• 0
3
votes
2
replies
648
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
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
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 6.1 years ago by
siklenkak
• 0
3
votes
4
replies
1.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw
chip-seq
histone
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
siklenkak
• 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
0
votes
1
reply
765
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
0
votes
3
replies
919
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
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
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
6
replies
1.4k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2
chip-seq
Differential binding
6.7 years ago
p2016k
• 0
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
0
replies
772
views
Job:
Post-doctoral position in algorithms for cancer data analysis
algorithms
ChIP-seq
cancer
Job
6.7 years ago
valentina.boeva
• 0
50 results • Page
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Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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