Showing : ChIP-seq • reset
1
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1
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308
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Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 15 months ago by ★ 4.3k • written 15 months ago by ▴ 20
0
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2
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305
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 18 months ago by ★ 4.3k • written 18 months ago by • 0
2
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7
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532
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Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 18 months ago by ★ 4.3k • written 18 months ago by ▴ 20
0
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1
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164
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Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 19 months ago by ★ 4.3k • written 20 months ago by ▴ 10
0
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1
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292
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use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 19 months ago by ★ 4.3k • written 21 months ago by • 0
0
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0
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207
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ChIPQC cross-coverage plot
chipqc chip-seq
21 months ago tuteja.reetu • 0
0
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0
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235
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
23 months ago Johannes Rainer ★ 1.9k
2
votes
1
reply
283
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 2.1 years ago by ★ 27k • written 2.1 years ago by ▴ 970
1
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4
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527
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 2.2 years ago by 58k • written 2.2 years ago by • 0
1
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4
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293
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 2.3 years ago by ★ 4.3k • written 2.3 years ago by • 0
1
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1
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331
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Diffbind with age as blocking factor
diffbind chip-seq
updated 2.3 years ago by ★ 4.3k • written 2.3 years ago by ▴ 10
0
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0
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942
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.6 years ago • updated 2.4 years ago Julie Zhu ★ 4.3k
2
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2
replies
757
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ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 2.4 years ago by ▴ 20 • written 2.9 years ago by ▴ 10
0
votes
1
reply
994
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 2.6 years ago by ★ 4.3k • written 2.6 years ago by • 0
0
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0
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433
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
3.1 years ago Ramiro Magno ▴ 100
2
votes
2
replies
554
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Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
3.2 years ago 2323982403 ▴ 50
0
votes
3
replies
380
views
normalization of ChIP-seq data
normalization chip-seq
3.2 years ago Bogdan ▴ 620
0
votes
4
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617
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csaw spike-in normalization
ChIP-seq csaw
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 260
0
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0
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439
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
3.3 years ago pierre.marin • 0
0
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2
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474
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csaw normalization and library size
chip-seq normalization
updated 3.5 years ago by ★ 27k • written 3.5 years ago by ▴ 260
0
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7
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971
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
3
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6
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787
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.5 years ago 94133 • 0
0
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5
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699
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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 3.7 years ago by ★ 27k • written 3.7 years ago by • 0
1
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1
reply
1.4k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
4.1 years ago chunhong.liu07 ▴ 10
0
votes
0
replies
710
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
4.2 years ago nbkingsley • 0
1
vote
5
replies
1.2k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 10 months ago by • 0 • written 4.3 years ago by ▴ 40
0
votes
2
replies
677
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 4.3 years ago by ★ 27k • written 4.3 years ago by • 0
1
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2
replies
773
views
Errors with makeTxDbFromBiomart
chip-seq
updated 4.3 years ago by 15k • written 4.3 years ago by • 0
0
votes
1
reply
921
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 4.4 years ago by ▴ 400 • written 4.5 years ago by • 0
2
votes
11
replies
1.4k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.5 years ago by 7.7k • written 4.5 years ago by • 0
2
votes
2
replies
760
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.5 years ago by ▴ 640 • written 4.5 years ago by ▴ 10
0
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1
reply
928
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.6 years ago by ★ 1.2k • written 4.6 years ago by • 0
0
votes
0
replies
551
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Meta-Analysis chip-seq data
chip-seq meta-analysis
4.6 years ago rezapanahi222 • 0
3
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2
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535
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statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 4.9 years ago by 13k • written 4.9 years ago by ▴ 620
0
votes
2
replies
1.0k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 5.0 years ago by ★ 4.3k • written 5.0 years ago by • 0
0
votes
3
replies
1.2k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 5.0 years ago by ★ 4.3k • written 5.0 years ago by • 0
3
votes
4
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1.1k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
3
votes
2
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1.4k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 10
0
votes
1
reply
652
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 5.4 years ago by ★ 4.3k • written 5.4 years ago by • 0
0
votes
3
replies
776
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 5.5 years ago by ★ 27k • written 5.5 years ago by • 0
0
votes
3
replies
2.8k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 5.5 years ago by ★ 4.3k • written 5.5 years ago by • 0
0
votes
2
replies
1.1k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 5.6 years ago by ★ 4.3k • written 5.6 years ago by • 0
0
votes
6
replies
1.2k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
5.6 years ago p2016k • 0
1
vote
18
replies
2.1k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 10
0
votes
0
replies
676
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
5.7 years ago valentina.boeva • 0
2
votes
1
reply
674
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 30
0
votes
0
replies
827
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
5.7 years ago Katja Hebestreit ▴ 130
0
votes
2
replies
1.3k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 6.0 years ago by ▴ 100 • written 7.0 years ago by • 0
0
votes
1
reply
1.5k
views
diffBind - bam not accessible
diffbind chip-seq bam
6.2 years ago eli7javasky • 0
3
votes
9
replies
1.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
6.4 years ago lindahove ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Answer: DiffBind issue: zero values for all peaks in one chromosome by Rory Stark ★ 4.3k
Losing the reads for one tissue on one chromosome doesn't sound too good! I notice that you are using `DiffBind_3.0`, which is out of da…
Votes
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
Comment: universalmotif, question about enrich_motifs function and number of hits returne
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