Showing : ChIP-seq • reset
3
votes
4
replies
299
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
6 weeks ago • updated 23 days ago spg • 0
0
votes
2
replies
236
views
HOMER error: Where is the file?
HOMER chip-seq
updated 3 months ago by ★ 2.1k • written 3 months ago by • 0
1
vote
2
replies
318
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
572
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 7 months ago by • 0 • written 8 months ago by ▴ 660
0
votes
1
reply
322
views
meta-gene profiles
ChIP-seq
updated 11 months ago by ▴ 60 • written 11 months ago by ▴ 660
1
vote
1
reply
539
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
2
replies
586
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
2
votes
7
replies
773
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 2.6 years ago by ▴ 20
0
votes
1
reply
284
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
1
reply
649
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 2.8 years ago by • 0
0
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0
replies
394
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ChIPQC cross-coverage plot
chipqc chip-seq
2.8 years ago tuteja.reetu • 0
0
votes
0
replies
389
views
Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
3.0 years ago Johannes Rainer ★ 2.0k
2
votes
1
reply
497
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
1
vote
4
replies
842
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 3.2 years ago by 62k • written 3.3 years ago by • 0
1
vote
4
replies
485
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
1
vote
1
reply
483
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
0
votes
0
replies
1.1k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
3.6 years ago • updated 3.4 years ago Julie Zhu ★ 4.3k
2
votes
2
replies
950
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
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
0
votes
0
replies
591
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
4.1 years ago Ramiro Magno ▴ 100
2
votes
2
replies
740
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
0
votes
3
replies
544
views
normalization of ChIP-seq data
normalization chip-seq
4.2 years ago Bogdan ▴ 660
0
votes
4
replies
827
views
csaw spike-in normalization
ChIP-seq csaw
updated 4.2 years ago by ★ 28k • written 4.3 years ago by ▴ 260
0
votes
0
replies
567
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
4.3 years ago pierre.marin • 0
0
votes
2
replies
629
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
7
replies
1.4k
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
3
votes
6
replies
994
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
4.5 years ago 94133 • 0
0
votes
5
replies
871
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
1
vote
1
reply
1.7k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
5.2 years ago chunhong.liu07 ▴ 10
0
votes
0
replies
851
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
5.2 years ago nbkingsley • 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
0
votes
2
replies
844
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
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
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
2
votes
2
replies
944
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 5.5 years ago by ▴ 650 • written 5.6 years ago by ▴ 10
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
0
votes
0
replies
662
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
5.6 years ago rezapanahi222 • 0
3
votes
2
replies
645
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
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
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
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
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
0
votes
1
reply
764
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
0
votes
3
replies
917
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
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
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
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
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
0
replies
769
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
6.7 years ago valentina.boeva • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: RUVr batch correction doubling number of DEGs by Michael Love 39k
No, this sounds like RUV is helping to reduce variance due to unaccounted for batch effects. So it’s helping.
Comment: Ascona Workshop “Biological systems: from first principles to data-​driven model by Wolfgang Huber 13k
Dear Liam, it's bi-annual, we just submitted a proposal. If it works out, it'll be in 2024, and as it looks now, in early September. Theme:…
Comment: IHW for multiple regression by Wolfgang Huber 13k
Indeed, for the two-sided t-test (and similar), the sign of the test statistic is independent of the p-value under the null hypothesis, and…
Comment: edgeR supports continuous covariates? by Jeffcgen2000 • 0
Hi Yunshun Chen and Gordon Smyth, does edgeR support mixed model? (https://en.wikipedia.org/wiki/Mixed_model)
Comment: find tandem repeats in DNA by me-nobody • 0
OK. Thank you very much!
Votes
A: edgeR: exactTest, glmFIt or glmQLFit approach?
Answer: on which data type limma::removeBatchEffect can be applyed?
C: WGCNA: Understanding module-trait correlations
A: WGCNA: Understanding module-trait correlations
A: Differential expression analysis starting from TPM data
Awards • All
Popular Question to Gordon Smyth 47k
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