Showing : ChIP-seq • reset
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
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
3
votes
9
replies
2.0k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
6.7 years ago lindahove ▴ 10
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
2
votes
7
replies
608
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
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
3
votes
6
replies
840
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
3.8 years ago 94133 • 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
5
replies
747
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
4
votes
4
replies
1.1k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
7.3 years ago IV ▴ 30
1
vote
4
replies
352
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
1
vote
4
replies
612
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
0
votes
4
replies
675
views
csaw spike-in normalization
ChIP-seq csaw
updated 3.6 years ago by ★ 27k • written 3.6 years ago by ▴ 260
0
votes
4
replies
123
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 2 days ago by ★ 1.2k • written 4 days ago by ▴ 640
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
3
replies
1.3k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 5.3 years ago by ★ 4.4k • written 5.4 years ago by • 0
0
votes
3
replies
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
0
votes
3
replies
810
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
0
votes
3
replies
420
views
normalization of ChIP-seq data
normalization chip-seq
3.5 years ago Bogdan ▴ 640
0
votes
2
replies
520
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
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
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
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 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 10
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
3
votes
2
replies
563
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
2
votes
2
replies
806
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
1
vote
2
replies
868
views
Errors with makeTxDbFromBiomart
chip-seq
updated 4.7 years ago by 15k • written 4.7 years ago by • 0
0
votes
2
replies
723
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
2
replies
599
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
2
votes
2
replies
809
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
0
votes
2
replies
378
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
0
votes
1
reply
976
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
2
votes
1
reply
707
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
1
vote
1
reply
370
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
2
votes
1
reply
350
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
0
votes
1
reply
352
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
0
votes
1
reply
200
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 23 months ago by ★ 4.4k • written 2.0 years ago by ▴ 10
0
votes
1
reply
1.6k
views
diffBind - bam not accessible
diffbind chip-seq bam
6.6 years ago eli7javasky • 0
0
votes
1
reply
951
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
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
0
votes
1
reply
983
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 4.9 years ago by ★ 1.2k • written 4.9 years ago by • 0
2
votes
1
reply
916
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
0
votes
1
reply
678
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
1
vote
1
reply
367
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
0
votes
1
reply
121
views
meta-gene profiles
ChIP-seq
updated 11 weeks ago by ▴ 40 • written 11 weeks ago by ▴ 640
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
0
votes
0
replies
582
views
Meta-Analysis chip-seq data
chip-seq meta-analysis
5.0 years ago rezapanahi222 • 0
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
0
replies
476
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
267
views
Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
2.3 years ago Johannes Rainer ★ 1.9k
50 results • Page 1 of 1
Recent ...
Replies
Comment: ROC plot for OPLS-DA by etienne.thevenot ▴ 20
I would suggest to concatenate your training and testing data rowwise, and to apply the `opls` method with the subset parameter to select t…
Comment: regression analysis for epic array methylation data using limma by nabiyogesh ▴ 10
Dear Basti, thank you so much! Could you please also help me how to arrange samples in the same order in rows (targests2) and columns in (…
Comment: How to figure out the FC value from Limma by ATpoint ★ 1.2k
You probably have opened that file in Excel before. Get it again directly from GEO2R, or even better take the R script GEO2R offers and run…
Comment: regression analysis for epic array methylation data using limma by Basti ▴ 280
The columns of your design matrix `var` corresponds to the coefficients that are fitted by limma. If you check your design matrix, you will…
Comment: How to figure out the FC value from Limma by beslinail • 0
I tried to FC column to dbl from chr. But FC colomn is changed by NA genlist_filter <- read_csv(file = "AD_control5.csv") gen…
Votes
Answer: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
A: Very low EdgeR Pvalues with very small sample size
A: Very low EdgeR Pvalues with very small sample size
Comment: Question on RNA-Seq single sample data analysis in EdgeR
Answer: Question on RNA-Seq single sample data analysis in EdgeR
Awards • All
Centurion to Basti ▴ 280
Scholar to Robert Castelo ★ 2.9k
Scholar to Gordon Smyth 45k
Popular Question to andrebolerbarros ▴ 10
Scholar to James W. MacDonald 59k
Locations • All
France, 1 minute ago
Norway, 1 minute ago
United Kingdom, 17 minutes ago
United Kingdom, 24 minutes ago
Norway, 25 minutes ago
Traffic: 432 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6