Showing : chip-seq • reset
3
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4
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RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
2.4 years ago • updated 2.3 years ago spg • 0
0
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2
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2.0k
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HOMER error: Where is the file?
HOMER chip-seq
updated 2.5 years ago by ★ 4.8k • written 2.5 years ago by • 0
1
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2
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1.3k
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Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
2.7 years ago etiennedanis • 0
0
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6
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2.3k
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performing the differential binding in ChIP-seq
ChIP-seq
updated 2.1 years ago by • 0 • written 2.9 years ago by ▴ 670
0
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1
reply
1.1k
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meta-gene profiles
ChIP-seq
updated 3.1 years ago by ▴ 60 • written 3.2 years ago by ▴ 670
1
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1
reply
1.3k
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Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 4.5 years ago by ★ 5.2k • written 4.5 years ago by ▴ 20
0
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2
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1.5k
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 4.8 years ago by ★ 5.2k • written 4.8 years ago by • 0
2
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7
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1.8k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 4.8 years ago by ★ 5.2k • written 4.8 years ago by ▴ 20
0
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1
reply
739
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Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by ▴ 10
0
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1
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1.7k
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use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 4.9 years ago by ★ 5.2k • written 5.0 years ago by ▴ 10
0
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0
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958
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ChIPQC cross-coverage plot
chipqc chip-seq
5.0 years ago tuteja.reetu • 0
0
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0
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959
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
5.2 years ago Johannes Rainer ★ 2.1k
2
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1
reply
1.3k
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Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ★ 4.8k
1
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4
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transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 10
1
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4
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1.4k
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 5.5 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
1
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1
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1.1k
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Diffbind with age as blocking factor
diffbind chip-seq
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by ▴ 10
0
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0
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1.7k
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Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
5.8 years ago • updated 5.7 years ago Julie Zhu ★ 4.3k
2
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2
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1.7k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 5.7 years ago by ▴ 20 • written 6.2 years ago by ▴ 10
0
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2
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3.9k
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Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 8 months ago by ▴ 20 • written 5.9 years ago by • 0
0
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0
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1.1k
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Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
6.4 years ago Ramiro Magno ▴ 100
2
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2
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1.5k
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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
6.4 years ago 2323982403 ▴ 60
0
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3
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1.1k
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normalization of ChIP-seq data
normalization chip-seq
6.5 years ago Bogdan ▴ 670
0
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4
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2.1k
views
csaw spike-in normalization
ChIP-seq csaw
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 260
0
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0
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1.1k
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How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
6.6 years ago pierre.marin • 0
0
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2
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1.4k
views
csaw normalization and library size
chip-seq normalization
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 260
0
votes
7
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2.8k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 6.7 years ago by • 0 • written 6.8 years ago by • 0
3
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6
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2.0k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
6.8 years ago 94133 • 0
0
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5
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1.8k
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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 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
1
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1
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2.7k
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Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
7.4 years ago chunhong.liu07 ▴ 10
0
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0
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1.4k
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ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
7.4 years ago nbkingsley • 0
1
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5
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2.9k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 4.1 years ago by • 0 • written 7.6 years ago by ▴ 40
0
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2
replies
1.5k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
1
vote
2
replies
1.9k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 7.6 years ago by 16k • written 7.6 years ago by • 0
0
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1
reply
1.7k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 7.7 years ago by ▴ 420 • written 7.8 years ago by • 0
3
votes
11
replies
2.9k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 7.7 years ago by ★ 7.9k • written 7.7 years ago by ▴ 10
2
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2
replies
1.8k
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 7.8 years ago by ▴ 670 • written 7.8 years ago by ▴ 10
0
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1
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1.8k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by • 0
0
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0
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996
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Meta-Analysis chip-seq data
chip-seq meta-analysis
7.9 years ago rezapanahi222 • 0
3
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2
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1.1k
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 8.2 years ago by ★ 13k • written 8.2 years ago by ▴ 670
0
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2
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1.9k
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Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 8.2 years ago by ★ 5.2k • written 8.2 years ago by • 0
0
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3
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2.4k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 8.3 years ago by ★ 5.2k • written 8.3 years ago by • 0
3
votes
4
replies
2.4k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 8.3 years ago by ★ 28k • written 8.3 years ago by • 0
4
votes
2
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2.8k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
0
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1
reply
1.3k
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 8.6 years ago by ★ 5.2k • written 8.6 years ago by • 0
0
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3
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1.8k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
votes
3
replies
4.7k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 8.7 years ago by ★ 5.2k • written 8.7 years ago by • 0
0
votes
6
replies
2.2k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
8.9 years ago p2016k • 0
1
vote
18
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4.1k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 10
0
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0
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1.2k
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Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
8.9 years ago valentina.boeva • 0
2
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1
reply
1.2k
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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