Showing : ChIP-seq • reset
3
votes
9
replies
2.2k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
7.4 years ago lindahove ▴ 10
2
votes
7
replies
769
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by ▴ 20
0
votes
7
replies
1.3k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 4.5 years ago by • 0 • written 4.5 years ago by • 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 • 0 • written 5.4 years ago by ▴ 40
1
vote
2
replies
1.0k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 5.4 years ago by 16k • written 5.4 years ago by • 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 ★ 4.6k • written 6.0 years ago by • 0
0
votes
6
replies
1.4k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
6.6 years ago p2016k • 0
1
vote
4
replies
484
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by • 0
0
votes
1
reply
761
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 6.4 years ago by ★ 4.6k • written 6.4 years ago by • 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 ★ 28k • written 6.3 years ago by ▴ 10
3
votes
4
replies
1.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
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 ★ 4.6k • written 6.0 years ago by • 0
3
votes
2
replies
643
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 5.9 years ago by 13k • written 5.9 years ago by ▴ 660
0
votes
1
reply
1.1k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 5.6 years ago by ★ 1.2k • written 5.6 years ago by • 0
2
votes
2
replies
939
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 5.5 years ago by ▴ 650 • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 5.4 years ago by ▴ 420 • written 5.5 years ago by • 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 7.8k • written 5.5 years ago by ▴ 10
3
votes
4
replies
296
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
6 weeks ago • updated 20 days ago spg • 0
0
votes
2
replies
1.5k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 7.0 years ago by ▴ 110 • written 8.0 years ago by • 0
4
votes
4
replies
1.2k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
8.0 years ago IV ▴ 30
2
votes
1
reply
774
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 30
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 ★ 28k • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 6.6 years ago by ★ 4.6k • written 6.6 years ago by • 0
0
votes
3
replies
3.2k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 6.5 years ago by ★ 4.6k • written 6.5 years ago by • 0
0
votes
3
replies
914
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
votes
1
reply
1.6k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 3.7 years ago by ★ 4.6k • written 3.7 years ago by • 0
1
vote
1
reply
481
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by ▴ 10
1
vote
4
replies
836
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 3.2 years ago by 62k • written 3.2 years ago by • 0
2
votes
1
reply
495
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ★ 2.1k
0
votes
1
reply
638
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 2.6 years ago by ★ 4.6k • written 2.7 years ago by • 0
0
votes
1
reply
281
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 2.6 years ago by ★ 4.6k • written 2.7 years ago by ▴ 10
0
votes
2
replies
581
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
1
vote
1
reply
536
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by ▴ 20
0
votes
1
reply
318
views
meta-gene profiles
ChIP-seq
updated 11 months ago by ▴ 60 • written 11 months ago by ▴ 660
1
vote
2
replies
316
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
6 months ago • updated 5 months ago etiennedanis • 0
0
votes
5
replies
568
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 7 months ago by • 0 • written 8 months ago by ▴ 660
0
votes
2
replies
228
views
HOMER error: Where is the file?
HOMER chip-seq
updated 12 weeks ago by ★ 2.1k • written 12 weeks ago by • 0
2
votes
1
reply
989
views
problem with characters in chromosome names in DiffBind dba
DiffBind ChIP-Seq
updated 8.2 years ago by ★ 4.6k • written 8.2 years ago by ▴ 120
0
votes
2
replies
843
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 ★ 28k • written 5.4 years ago by • 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
5.1 years ago chunhong.liu07 ▴ 10
0
votes
5
replies
869
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 ★ 28k • written 4.7 years ago by • 0
0
votes
2
replies
627
views
csaw normalization and library size
chip-seq normalization
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 260
0
votes
4
replies
823
views
csaw spike-in normalization
ChIP-seq csaw
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 260
2
votes
2
replies
739
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
2
votes
2
replies
947
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 ▴ 20 • written 3.9 years ago by ▴ 10
0
votes
0
replies
659
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
5.6 years ago rezapanahi222 • 0
0
votes
0
replies
767
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
6.7 years ago valentina.boeva • 0
0
votes
0
replies
590
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
4.1 years ago Ramiro Magno ▴ 100
0
votes
0
replies
850
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
5.2 years ago nbkingsley • 0
0
votes
0
replies
390
views
ChIPQC cross-coverage plot
chipqc chip-seq
2.8 years ago tuteja.reetu • 0
50 results • Page 1 of 1
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Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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