Showing : chip-seq • reset
3
votes
4
replies
324
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
7 weeks ago • updated 4 weeks ago spg • 0
0
votes
2
replies
258
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
328
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
6 months ago etiennedanis • 0
0
votes
5
replies
587
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
327
views
meta-gene profiles
ChIP-seq
updated 11 months ago by ▴ 60 • written 11 months ago by ▴ 660
1
vote
1
reply
541
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
590
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
777
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 2.6 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 2.7 years ago by ★ 4.6k • written 2.7 years ago by ▴ 10
0
votes
1
reply
681
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 2.7 years ago by ★ 4.6k • written 2.8 years ago by • 0
0
votes
0
replies
396
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ChIPQC cross-coverage plot
chipqc chip-seq
2.8 years ago tuteja.reetu • 0
0
votes
0
replies
392
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
502
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
850
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 3.3 years ago by 62k • written 3.3 years ago by • 0
1
vote
4
replies
491
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
486
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 3.5 years ago Julie Zhu ★ 4.3k
2
votes
2
replies
954
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 4.0 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
594
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
4.2 years ago Ramiro Magno ▴ 100
2
votes
2
replies
747
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
546
views
normalization of ChIP-seq data
normalization chip-seq
4.3 years ago Bogdan ▴ 660
0
votes
4
replies
835
views
csaw spike-in normalization
ChIP-seq csaw
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 260
0
votes
0
replies
570
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
630
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
1.0k
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
872
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
857
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
846
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
1.1k
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 5.5 years ago by ▴ 420 • written 5.5 years ago by • 0
3
votes
11
replies
1.8k
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
946
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 5.6 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 5.7 years ago by • 0
0
votes
0
replies
670
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
5.7 years ago rezapanahi222 • 0
3
votes
2
replies
650
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 6.1 years ago by ★ 4.6k • written 6.1 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 6.1 years ago by ★ 28k • written 6.1 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
766
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
920
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
6.7 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
775
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
Comment: TCGA: clinical data and expression data by sharifnstu1203002m • 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Jonathan Göke ▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R by Gordon Smyth 47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user) by lalanis1 • 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma by Gordon Smyth 47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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