Showing : chip-seq • reset
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
16 months ago spg • 0
0
votes
2
replies
1.3k
views
HOMER error: Where is the file?
HOMER chip-seq
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
1
vote
2
replies
943
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
21 months ago etiennedanis • 0
0
votes
6
replies
1.7k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 13 months ago by • 0 • written 23 months ago by ▴ 670
0
votes
1
reply
734
views
meta-gene profiles
ChIP-seq
updated 2.2 years ago by ▴ 60 • written 2.2 years ago by ▴ 670
1
vote
1
reply
931
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by ▴ 20
0
votes
2
replies
1.1k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by ▴ 20
0
votes
1
reply
509
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 3.9 years ago by ★ 5.2k • written 4.0 years ago by ▴ 10
0
votes
1
reply
1.3k
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 3.9 years ago by ★ 5.2k • written 4.0 years ago by ▴ 10
0
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0
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701
views
ChIPQC cross-coverage plot
chipqc chip-seq
4.0 years ago tuteja.reetu • 0
0
votes
0
replies
744
views
Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
4.2 years ago Johannes Rainer ★ 2.0k
2
votes
1
reply
942
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ★ 4.1k
1
vote
4
replies
1.3k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
1
vote
4
replies
899
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
1
vote
1
reply
829
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
4.8 years ago • updated 4.7 years ago Julie Zhu ★ 4.3k
2
votes
2
replies
1.3k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 4.7 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
0
votes
1
reply
2.7k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
0
votes
0
replies
882
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
5.4 years ago Ramiro Magno ▴ 100
2
votes
2
replies
1.2k
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
5.5 years ago 2323982403 ▴ 60
0
votes
3
replies
856
views
normalization of ChIP-seq data
normalization chip-seq
5.5 years ago Bogdan ▴ 670
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 260
0
votes
0
replies
912
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
5.6 years ago pierre.marin • 0
0
votes
2
replies
1.0k
views
csaw normalization and library size
chip-seq normalization
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 260
0
votes
7
replies
2.2k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
0
votes
5
replies
1.4k
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 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
1
vote
1
reply
2.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
6.4 years ago chunhong.liu07 ▴ 10
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
6.4 years ago nbkingsley • 0
1
vote
5
replies
2.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 3.1 years ago by • 0 • written 6.6 years ago by ▴ 40
0
votes
2
replies
1.2k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
1
vote
2
replies
1.6k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.6 years ago by 16k • written 6.6 years ago by • 0
0
votes
1
reply
1.5k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 6.7 years ago by ▴ 420 • written 6.8 years ago by • 0
3
votes
11
replies
2.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 10
2
votes
2
replies
1.4k
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 6.8 years ago by ▴ 650 • written 6.8 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
0
votes
0
replies
850
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
6.9 years ago rezapanahi222 • 0
3
votes
2
replies
901
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 7.2 years ago by ★ 13k • written 7.2 years ago by ▴ 670
0
votes
2
replies
1.6k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 7.2 years ago by ★ 5.2k • written 7.3 years ago by • 0
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
4
votes
2
replies
2.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
0
votes
1
reply
1.0k
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 7.7 years ago by ★ 5.2k • written 7.7 years ago by • 0
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
0
votes
3
replies
4.0k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
4
replies
1.9k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
6
replies
1.8k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
7.9 years ago p2016k • 0
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
0
votes
0
replies
985
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
7.9 years ago valentina.boeva • 0
50 results • Page 1 of 1
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Replies
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank" by James W. MacDonald 65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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