Showing : ChIP-seq • reset
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15
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performing the differential binding in ChIP-seq
ChIP-seq
15 hours ago Bogdan ▴ 640
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1
reply
119
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meta-gene profiles
ChIP-seq
updated 11 weeks ago by ▴ 40 • written 11 weeks ago by ▴ 640
1
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1
reply
360
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Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 19 months ago by ★ 4.4k • written 19 months ago by ▴ 20
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2
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371
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 22 months ago by ★ 4.4k • written 22 months ago by • 0
2
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7
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598
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Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 22 months ago by ★ 4.4k • written 22 months ago by ▴ 20
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1
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197
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Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 23 months ago by ★ 4.4k • written 2.0 years ago by ▴ 10
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1
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344
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use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 23 months ago by ★ 4.4k • written 2.1 years ago by • 0
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0
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259
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ChIPQC cross-coverage plot
chipqc chip-seq
2.1 years ago tuteja.reetu • 0
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0
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263
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
2.3 years ago Johannes Rainer ★ 1.9k
2
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1
reply
349
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Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 2.4 years ago by ★ 27k • written 2.4 years ago by ★ 1.2k
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4
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606
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transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 2.6 years ago by 59k • written 2.6 years ago by • 0
1
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4
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343
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 2.6 years ago by ★ 4.4k • written 2.6 years ago by • 0
1
vote
1
reply
368
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Diffbind with age as blocking factor
diffbind chip-seq
updated 2.6 years ago by ★ 4.4k • written 2.6 years ago by ▴ 10
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0
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1000
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Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.9 years ago • updated 2.8 years ago Julie Zhu ★ 4.3k
2
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2
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807
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ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 2.8 years ago by ▴ 20 • written 3.2 years ago by ▴ 10
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1
reply
1.2k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 3.0 years ago by ★ 4.4k • written 3.0 years ago by • 0
0
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0
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469
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
3.4 years ago Ramiro Magno ▴ 100
2
votes
2
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597
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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
3.5 years ago 2323982403 ▴ 50
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3
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416
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normalization of ChIP-seq data
normalization chip-seq
3.5 years ago Bogdan ▴ 640
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4
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673
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csaw spike-in normalization
ChIP-seq csaw
updated 3.6 years ago by ★ 27k • written 3.6 years ago by ▴ 260
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0
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476
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How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
3.6 years ago pierre.marin • 0
0
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2
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519
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csaw normalization and library size
chip-seq normalization
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 260
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7
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1.1k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
3
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6
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833
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.8 years ago 94133 • 0
0
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5
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744
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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 4.0 years ago by ★ 27k • written 4.0 years ago by • 0
1
vote
1
reply
1.5k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
4.5 years ago chunhong.liu07 ▴ 10
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0
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750
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ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
4.5 years ago nbkingsley • 0
1
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5
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1.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 14 months ago by • 0 • written 4.7 years ago by ▴ 40
0
votes
2
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720
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Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 4.7 years ago by ★ 27k • written 4.7 years ago by • 0
1
vote
2
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865
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Errors with makeTxDbFromBiomart
chip-seq
updated 4.7 years ago by 15k • written 4.7 years ago by • 0
0
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1
reply
972
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 4.7 years ago by ▴ 400 • written 4.8 years ago by • 0
2
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11
replies
1.5k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.8 years ago by 7.8k • written 4.8 years ago by • 0
2
votes
2
replies
804
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.8 years ago by ▴ 640 • written 4.9 years ago by ▴ 10
0
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1
reply
982
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.9 years ago by ★ 1.2k • written 4.9 years ago by • 0
0
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0
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580
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Meta-Analysis chip-seq data
chip-seq meta-analysis
4.9 years ago rezapanahi222 • 0
3
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2
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562
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statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 5.2 years ago by 13k • written 5.2 years ago by ▴ 640
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2
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1.1k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 5.3 years ago by ★ 4.4k • written 5.3 years ago by • 0
0
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3
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1.3k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 5.3 years ago by ★ 4.4k • written 5.3 years ago by • 0
3
votes
4
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1.2k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 5.4 years ago by ★ 27k • written 5.4 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 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 10
0
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1
reply
677
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 5.7 years ago by ★ 4.4k • written 5.7 years ago by • 0
0
votes
3
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808
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 5.8 years ago by ★ 27k • written 5.8 years ago by • 0
0
votes
3
replies
2.9k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 5.8 years ago by ★ 4.4k • written 5.8 years ago by • 0
0
votes
2
replies
1.1k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 5.9 years ago by ★ 4.4k • written 5.9 years ago by • 0
0
votes
6
replies
1.3k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
5.9 years ago p2016k • 0
1
vote
18
replies
2.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 6.0 years ago by ★ 27k • written 6.0 years ago by ▴ 10
0
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0
replies
699
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
6.0 years ago valentina.boeva • 0
2
votes
1
reply
707
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 6.0 years ago by ★ 27k • written 6.0 years ago by ▴ 30
0
votes
0
replies
867
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
6.0 years ago Katja Hebestreit ▴ 130
0
votes
2
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1.4k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 6.3 years ago by ▴ 100 • written 7.3 years ago by • 0
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Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Yang Shi • 0
Thanks sir! I got it now!
Comment: Reading multiple data segments from FCS 3.0 file by SamGG ▴ 270
You should better start a question, but here is some clues. While this operation is refered as concatenate you can find it as coerce in flo…
Answer: how to make a group to apply the data to CAMERA by Gordon Smyth 45k
See the [limma User's Guide](https://www.bioconductor.org/packages/3.15/bioc/vignettes/limma/inst/doc/usersguide.pdf) for how to undertake …
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Guido Hooiveld ★ 3.2k
To add to the extensive discussion above, you may also want to have a look at the so-called UPC algorithm, available in the [package][1] `S…
Answer: How to best visualize multi-level transcriptomics experiment data? by Gordon Smyth 45k
> One way is to extract the differentially expressed genes with p.val = 0.05 and logFC = +/-1.0 I strongly recommend using FDR < 0.05 and…
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Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
A: coefficient not estimable (limma warning)
A: coefficient not estimable (limma warning)
A: conceptual question about FDR, FDR adjusted p-value and q-value
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