Showing : chip-seq • reset
1
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1
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228
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Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
0
votes
2
replies
187
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
2
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7
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366
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Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
0
votes
1
reply
104
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 13 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
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1
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160
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use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 13 months ago by ★ 4.0k • written 15 months ago by • 0
0
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0
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131
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ChIPQC cross-coverage plot
chipqc chip-seq
15 months ago tuteja.reetu • 0
0
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0
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145
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Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
17 months ago Johannes Rainer ★ 1.9k
2
votes
1
reply
191
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 700
1
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4
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374
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transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 21 months ago by 57k • written 21 months ago by • 0
1
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4
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204
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in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
1
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1
reply
261
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 21 months ago by ★ 4.0k • written 21 months ago by ▴ 10
0
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0
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852
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.1 years ago • updated 23 months ago Julie Zhu ★ 4.3k
2
votes
2
replies
596
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ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 23 months ago by ▴ 20 • written 2.4 years ago by ▴ 10
0
votes
1
reply
691
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 2.2 years ago by ★ 4.0k • written 2.2 years ago by • 0
0
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0
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367
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
2.6 years ago Ramiro Magno ▴ 100
2
votes
2
replies
459
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
2.7 years ago 2323982403 ▴ 50
0
votes
3
replies
319
views
normalization of ChIP-seq data
normalization chip-seq
2.7 years ago Bogdan ▴ 620
0
votes
4
replies
505
views
csaw spike-in normalization
ChIP-seq csaw
updated 2.7 years ago by ★ 27k • written 2.7 years ago by ▴ 260
0
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0
replies
312
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How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
2.8 years ago pierre.marin • 0
0
votes
2
replies
415
views
csaw normalization and library size
chip-seq normalization
updated 3.0 years ago by ★ 27k • written 3.0 years ago by ▴ 260
0
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7
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766
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.0 years ago by • 0 • written 3.0 years ago by • 0
3
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6
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675
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.0 years ago 94133 • 0
0
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5
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612
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 3.2 years ago by ★ 27k • written 3.2 years ago by • 0
1
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1
reply
1.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
3.6 years ago chunhong.liu07 ▴ 10
0
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0
replies
617
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
3.7 years ago nbkingsley • 0
1
vote
5
replies
999
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 4 months ago by • 0 • written 3.9 years ago by ▴ 40
0
votes
2
replies
589
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 3.8 years ago by ★ 27k • written 3.8 years ago by • 0
1
vote
2
replies
679
views
Errors with makeTxDbFromBiomart
chip-seq
updated 3.9 years ago by 15k • written 3.9 years ago by • 0
0
votes
1
reply
832
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 3.9 years ago by ▴ 400 • written 4.0 years ago by • 0
2
votes
11
replies
1.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.0 years ago by 7.6k • written 4.0 years ago by • 0
2
votes
2
replies
640
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.0 years ago by ▴ 630 • written 4.0 years ago by ▴ 10
0
votes
1
reply
836
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.1 years ago by ★ 1.2k • written 4.1 years ago by • 0
0
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0
replies
501
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
4.1 years ago rezapanahi222 • 0
3
votes
2
replies
484
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 4.4 years ago by 13k • written 4.4 years ago by ▴ 620
0
votes
2
replies
918
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 4.5 years ago by ★ 4.0k • written 4.5 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 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
3
votes
4
replies
988
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 4.5 years ago by ★ 27k • written 4.5 years ago by • 0
3
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2
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1.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 4.8 years ago by ★ 27k • written 4.8 years ago by ▴ 10
0
votes
1
reply
609
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
0
votes
3
replies
725
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
0
votes
3
replies
2.5k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
votes
2
replies
866
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
0
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6
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1.1k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
5.1 years ago p2016k • 0
1
vote
18
replies
1.9k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 10
0
votes
0
replies
634
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
5.2 years ago valentina.boeva • 0
2
votes
1
reply
614
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 30
0
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0
replies
748
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
5.2 years ago Katja Hebestreit ▴ 130
0
votes
2
replies
1.3k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 5.5 years ago by ▴ 100 • written 6.5 years ago by • 0
0
votes
1
reply
1.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
5.7 years ago eli7javasky • 0
3
votes
9
replies
1.7k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
5.9 years ago lindahove ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: error in getBM (biomaRt): "error: no such table: metadata" by Aravind Easwar • 0
I faced a similar issue. In my case, none of the biomaRt functions worked and all threw the same error. `Error: no such table: metadata` …
Comment: Accession ID Conversion and Missing Results by James W. MacDonald 57k
If there were a simple way around this I would have told you rather than explain why it doesn't do what you expect. I mean, what's the prof…
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Michael Love 33k
I would set reference levels for all factors in the design.
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Hi, Michael: Really appreciated your input and advice! For the first question, I did used "WT" for my second way of modle setting althoug…
Comment: Error in .testForValidKeys "org.At.tair.db" by James W. MacDonald 57k
I must have hit Enter too soon, so you should come to the support site to see my full answer.
Votes
C: DESeq2 design formula: single control for multiple conditions [RIP-seq]
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Answer: cannot install edgeR on M1 Mac
Answer: cannot install edgeR on M1 Mac
Answer: problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignmen
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Scholar to James W. MacDonald 57k
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