Showing : ChIP-seq • reset
0
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3
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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
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
3
votes
9
replies
2.0k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
6.7 years ago lindahove ▴ 10
0
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1
reply
1.6k
views
diffBind - bam not accessible
diffbind chip-seq bam
6.6 years ago eli7javasky • 0
2
votes
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
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
3
votes
2
replies
1.5k
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
votes
2
replies
1.4k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 6.3 years ago by ▴ 100 • written 7.3 years ago by • 0
1
vote
5
replies
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
3
replies
1.3k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 5.4 years ago by ★ 4.4k • written 5.4 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
6.0 years ago p2016k • 0
0
votes
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
3
votes
4
replies
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
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
2
replies
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
votes
7
replies
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
4
votes
4
replies
1.1k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
7.3 years ago IV ▴ 30
0
votes
0
replies
1.0k
views
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
0
votes
1
reply
985
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.9 years ago by ★ 1.2k • written 5.0 years ago by • 0
0
votes
1
reply
977
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 4.8 years ago by ▴ 400 • written 4.8 years ago by • 0
0
votes
1
reply
952
views
News: Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course RNA-Seq Chip-seq Parallel News
7.2 years ago Martin Morgan 25k
2
votes
1
reply
920
views
problem with characters in chromosome names in DiffBind dba
DiffBind ChIP-Seq
updated 7.5 years ago by ★ 4.4k • written 7.5 years ago by ▴ 120
1
vote
2
replies
874
views
Errors with makeTxDbFromBiomart
chip-seq
updated 4.7 years ago by 15k • written 4.7 years ago by • 0
0
votes
0
replies
872
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
6.1 years ago Katja Hebestreit ▴ 130
3
votes
6
replies
842
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.8 years ago 94133 • 0
0
votes
3
replies
811
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
2
votes
2
replies
811
views
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 3.3 years ago by ▴ 10
2
votes
2
replies
808
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.9 years ago by ▴ 640 • written 4.9 years ago by ▴ 10
0
votes
0
replies
755
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
4.5 years ago nbkingsley • 0
0
votes
5
replies
750
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 4.0 years ago by ★ 27k • written 4.0 years ago by • 0
0
votes
2
replies
724
views
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
2
votes
1
reply
709
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
702
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
6.0 years ago valentina.boeva • 0
0
votes
1
reply
679
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
4
replies
678
views
csaw spike-in normalization
ChIP-seq csaw
updated 3.6 years ago by ★ 27k • written 3.6 years ago by ▴ 260
1
vote
4
replies
615
views
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
2
votes
7
replies
609
views
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
2
votes
2
replies
603
views
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
0
votes
0
replies
584
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
5.0 years ago rezapanahi222 • 0
3
votes
2
replies
564
views
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
0
votes
2
replies
522
views
csaw normalization and library size
chip-seq normalization
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 260
0
votes
0
replies
477
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
3.6 years ago pierre.marin • 0
0
votes
0
replies
471
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
3.5 years ago Ramiro Magno ▴ 100
0
votes
3
replies
421
views
normalization of ChIP-seq data
normalization chip-seq
3.6 years ago Bogdan ▴ 640
0
votes
2
replies
379
views
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
1
vote
1
reply
371
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 2.6 years ago by ★ 4.4k • written 2.6 years ago by ▴ 10
1
vote
1
reply
368
views
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
1
vote
4
replies
355
views
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
0
votes
1
reply
353
views
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
2
votes
1
reply
351
views
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
50 results • Page 1 of 1
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Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI() by Lan Anh • 0
Hello, Sorry for the late answer, I called several packages after my error and I do not know how it worked after that. Thank you for the h…
Comment: LogFC values in edgeR - w/wo intercept by JK Kim • 0
Thanks, Dr. Smyth!
Comment: LogFC values in edgeR - w/wo intercept by JK Kim • 0
Oops. I just corrected the URL. Thank you Dr. Smyth.
Comment: Fail to run RupRadar by Qingwei • 0
Dear Sergi, Yeah, it works. ```r dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads, GTF.featureType="cDNA_match", GTF.attrType="ID…
Comment: LogFC values in edgeR - w/wo intercept by Gordon Smyth 45k
The link you've entered for "A guide to creating design matrices for gene expression experiments" doesn't work. Could you please correct th…
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Comment: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: LogFC values in edgeR - w/wo intercept
Answer: broken chain import in liftOver
Answer: toGRanges help!
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