Showing : ChIP-seq • reset
3
votes
9
replies
1.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
6.4 years ago lindahove ▴ 10
2
votes
7
replies
532
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 18 months ago by ★ 4.3k • written 18 months ago by ▴ 20
0
votes
7
replies
973
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
1
vote
5
replies
1.2k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 10 months ago by • 0 • written 4.4 years ago by ▴ 40
1
vote
2
replies
773
views
Errors with makeTxDbFromBiomart
chip-seq
updated 4.3 years ago by 15k • written 4.4 years ago by • 0
0
votes
3
replies
1.2k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 5.0 years ago by ★ 4.3k • written 5.0 years ago by • 0
0
votes
6
replies
1.2k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
5.6 years ago p2016k • 0
1
vote
4
replies
293
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 2.3 years ago by ★ 4.3k • written 2.3 years ago by • 0
0
votes
1
reply
652
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 5.4 years ago by ★ 4.3k • written 5.4 years ago by • 0
3
votes
2
replies
1.4k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 10
3
votes
4
replies
1.1k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 5.0 years ago by ★ 27k • written 5.0 years ago by • 0
0
votes
2
replies
1.0k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 5.0 years ago by ★ 4.3k • written 5.0 years ago by • 0
3
votes
2
replies
535
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 4.9 years ago by 13k • written 4.9 years ago by ▴ 620
0
votes
1
reply
929
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.6 years ago by ★ 1.2k • written 4.6 years ago by • 0
2
votes
2
replies
761
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 4.5 years ago by ▴ 640 • written 4.5 years ago by ▴ 10
0
votes
1
reply
924
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 4.4 years ago by ▴ 400 • written 4.5 years ago by • 0
2
votes
11
replies
1.4k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 4.5 years ago by 7.7k • written 4.5 years ago by • 0
0
votes
1
reply
999
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 2.7 years ago by ★ 4.3k • written 2.7 years ago by • 0
0
votes
2
replies
1.3k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 6.0 years ago by ▴ 100 • written 7.0 years ago by • 0
4
votes
4
replies
996
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
7.0 years ago IV ▴ 30
2
votes
1
reply
674
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 30
1
vote
18
replies
2.1k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 5.7 years ago by ★ 27k • written 5.7 years ago by ▴ 10
0
votes
2
replies
1.1k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 5.6 years ago by ★ 4.3k • written 5.6 years ago by • 0
0
votes
3
replies
2.8k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 5.5 years ago by ★ 4.3k • written 5.5 years ago by • 0
0
votes
3
replies
777
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 5.5 years ago by ★ 27k • written 5.5 years ago by • 0
0
votes
5
replies
700
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 3.7 years ago by ★ 27k • written 3.7 years ago by • 0
0
votes
2
replies
474
views
csaw normalization and library size
chip-seq normalization
updated 3.5 years ago by ★ 27k • written 3.5 years ago by ▴ 260
0
votes
4
replies
619
views
csaw spike-in normalization
ChIP-seq csaw
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 260
2
votes
2
replies
555
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
3.2 years ago 2323982403 ▴ 50
2
votes
2
replies
758
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 2.4 years ago by ▴ 20 • written 2.9 years ago by ▴ 10
2
votes
1
reply
896
views
problem with characters in chromosome names in DiffBind dba
DiffBind ChIP-Seq
updated 7.1 years ago by ★ 4.3k • written 7.2 years ago by ▴ 120
1
vote
1
reply
331
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 2.3 years ago by ★ 4.3k • written 2.3 years ago by ▴ 10
1
vote
4
replies
528
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 2.2 years ago by 58k • written 2.2 years ago by • 0
2
votes
1
reply
283
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 2.1 years ago by ★ 27k • written 2.1 years ago by ▴ 970
0
votes
1
reply
293
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 19 months ago by ★ 4.3k • written 21 months ago by • 0
0
votes
1
reply
164
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 19 months ago by ★ 4.3k • written 20 months ago by ▴ 10
0
votes
2
replies
305
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 18 months ago by ★ 4.3k • written 18 months ago by • 0
1
vote
1
reply
309
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 15 months ago by ★ 4.3k • written 15 months ago by ▴ 20
0
votes
2
replies
678
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 4.3 years ago by ★ 27k • written 4.3 years ago by • 0
1
vote
1
reply
1.4k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
4.1 years ago chunhong.liu07 ▴ 10
0
votes
0
replies
552
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
4.6 years ago rezapanahi222 • 0
0
votes
0
replies
677
views
Job: Post-doctoral position in algorithms for cancer data analysis
algorithms ChIP-seq cancer Job
5.7 years ago valentina.boeva • 0
0
votes
0
replies
435
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
3.1 years ago Ramiro Magno ▴ 100
0
votes
0
replies
710
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
4.2 years ago nbkingsley • 0
0
votes
0
replies
208
views
ChIPQC cross-coverage plot
chipqc chip-seq
21 months ago tuteja.reetu • 0
0
votes
1
reply
915
views
News: Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course RNA-Seq Chip-seq Parallel News
6.9 years ago Martin Morgan 25k
3
votes
6
replies
787
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.5 years ago 94133 • 0
0
votes
0
replies
827
views
Job: Bioinformatics position at the Department of Genetics, Stanford, California
next-generation sequencing rna-seq chip-seq single cell Job
5.7 years ago Katja Hebestreit ▴ 130
0
votes
0
replies
945
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
2.6 years ago • updated 2.4 years ago Julie Zhu ★ 4.3k
0
votes
0
replies
439
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
3.3 years ago pierre.marin • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Uniform window size for different genes by rbenel ▴ 20
Thanks, I'll keep working on it because the `png("two_transcripts.ong", 240)` still looks a bit weird... thanks though!
Comment: DTU using DEXSeq (time series data with condition factor) by Alejandro Reyes ★ 1.8k
Apologies for late reply, Nirad. You probably figured it out by now. In the formulae, the 'exon' term would take the baseline transcript us…
Comment: DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ens by Alejandro Reyes ★ 1.8k
Apologies for late reply. Could you share the link to the gtf source?
Answer: Normalizing exonic reads and then log transforming or variance stabilising by Alejandro Reyes ★ 1.8k
Hello. Short answer is yes, count-level transoformation for variance stabilization also work for exon-count level matrices.
Comment: A mistake came when I install some packages using "biocmanager" by f1014063507 • 0
Thanks for answering. In fact, I can use the computer to install packages by "install.packages()", but the "biocmanager::install()" doesn'…
Votes
Answer: Joint disperstion estimation for DEXSeq and DESeq2
Answer: Problems to find the pvalues via rowttests
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
A: How to use subSeq with DNAStringSet and information of GroupedIRanges?
Annotating GRanges with TxDb gene models using plyranges
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