Showing : ChIP-seq • reset
1
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1
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254
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Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
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2
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225
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
2
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7
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409
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Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
126
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 15 months ago by ★ 4.1k • written 16 months ago by ▴ 10
0
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1
reply
213
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use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 15 months ago by ★ 4.1k • written 16 months ago by • 0
0
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0
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157
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ChIPQC cross-coverage plot
chipqc chip-seq
17 months ago tuteja.reetu • 0
0
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0
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178
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
19 months ago Johannes Rainer ★ 1.9k
2
votes
1
reply
220
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 830
1
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4
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427
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transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 22 months ago by 58k • written 23 months ago by • 0
1
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4
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230
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
1
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1
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291
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Diffbind with age as blocking factor
diffbind chip-seq
updated 23 months ago by ★ 4.1k • written 23 months ago by ▴ 10
0
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0
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894
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.2 years ago • updated 2.1 years ago Julie Zhu ★ 4.3k
2
votes
2
replies
640
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ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 2.1 years ago by ▴ 20 • written 2.6 years ago by ▴ 10
0
votes
1
reply
800
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by • 0
0
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0
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389
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
2.8 years ago Ramiro Magno ▴ 100
2
votes
2
replies
491
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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
2.9 years ago 2323982403 ▴ 50
0
votes
3
replies
341
views
normalization of ChIP-seq data
normalization chip-seq
2.9 years ago Bogdan ▴ 620
0
votes
4
replies
546
views
csaw spike-in normalization
ChIP-seq csaw
updated 2.9 years ago by ★ 27k • written 2.9 years ago by ▴ 260
0
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0
replies
376
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
3.0 years ago pierre.marin • 0
0
votes
2
replies
434
views
csaw normalization and library size
chip-seq normalization
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 260
0
votes
7
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821
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.2 years ago by • 0 • written 3.2 years ago by • 0
3
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6
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725
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.2 years ago 94133 • 0
0
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5
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642
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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 3.3 years ago by ★ 27k • written 3.3 years ago by • 0
1
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1
reply
1.3k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
3.8 years ago chunhong.liu07 ▴ 10
0
votes
0
replies
641
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
3.8 years ago nbkingsley • 0
1
vote
5
replies
1.1k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 6 months ago by • 0 • written 4.0 years ago by ▴ 40
0
votes
2
replies
623
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 4.0 years ago by ★ 27k • written 4.0 years ago by • 0
1
vote
2
replies
717
views
Errors with makeTxDbFromBiomart
chip-seq
updated 4.0 years ago by 15k • written 4.0 years ago by • 0
0
votes
1
reply
860
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 4.1 years ago by ▴ 400 • written 4.2 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 4.1 years ago by 7.6k • written 4.1 years ago by • 0
2
votes
2
replies
667
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.2 years ago by ▴ 640 • written 4.2 years ago by ▴ 10
0
votes
1
reply
879
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.3 years ago by ★ 1.2k • written 4.3 years ago by • 0
0
votes
0
replies
524
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
4.3 years ago rezapanahi222 • 0
3
votes
2
replies
504
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 4.6 years ago by 13k • written 4.6 years ago by ▴ 620
0
votes
2
replies
953
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 4.6 years ago by ★ 4.1k • written 4.6 years ago by • 0
0
votes
3
replies
1.1k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 4.7 years ago by ★ 4.1k • written 4.7 years ago by • 0
3
votes
4
replies
1.0k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 4.7 years ago by ★ 27k • written 4.7 years ago by • 0
3
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2
replies
1.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 4.9 years ago by ★ 27k • written 4.9 years ago by ▴ 10
0
votes
1
reply
625
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 5.0 years ago by ★ 4.1k • written 5.0 years ago by • 0
0
votes
3
replies
749
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 5.1 years ago by ★ 27k • written 5.1 years ago by • 0
0
votes
3
replies
2.6k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 5.1 years ago by ★ 4.1k • written 5.1 years ago by • 0
0
votes
2
replies
945
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 5.2 years ago by ★ 4.1k • written 5.2 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
5.3 years ago p2016k • 0
1
vote
18
replies
2.0k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 10
0
votes
0
replies
655
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
5.3 years ago valentina.boeva • 0
2
votes
1
reply
635
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.4 years ago by ★ 27k • written 5.4 years ago by ▴ 30
0
votes
0
replies
775
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
5.4 years ago Katja Hebestreit ▴ 130
0
votes
2
replies
1.3k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 5.6 years ago by ▴ 100 • written 6.7 years ago by • 0
0
votes
1
reply
1.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
5.9 years ago eli7javasky • 0
3
votes
9
replies
1.8k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
6.0 years ago lindahove ▴ 10
50 results • Page 1 of 1
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Answer: Effect size using likelihood ratio test in DESeq2 by ATpoint ▴ 830
The thing with time-courses is that you do not necessarily have binary patterns of gene expression changes being only up-or downregulated. …
Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
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Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
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Answer: Degust: what normalization method does it use
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