Showing : Chip-Seq • reset
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
9.2 years ago IV ▴ 30
4
votes
2
replies
2.3k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
3
votes
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
8.7 years ago lindahove ▴ 10
3
votes
11
replies
2.3k
views
Exporting normalized counts over final DB windows from csaw
csaw edger chip-seq
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 10
3
votes
2
replies
901
views
statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
chip-seq
updated 7.2 years ago by ★ 13k • written 7.2 years ago by ▴ 670
3
votes
4
replies
1.9k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
3
votes
4
replies
1.6k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
16 months ago spg • 0
3
votes
6
replies
1.6k
views
ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
5.8 years ago 94133 • 0
2
votes
1
reply
1.2k
views
problem with characters in chromosome names in DiffBind dba
DiffBind ChIP-Seq
updated 9.4 years ago by ★ 5.2k • written 9.4 years ago by ▴ 120
2
votes
1
reply
998
views
How does csaw handle multiply aligned reads?
csaw chip-seq
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
2
votes
2
replies
1.4k
views
How to use Diffbind as complete beginner?
diffbind chip-seq
updated 6.8 years ago by ▴ 650 • written 6.8 years ago by ▴ 10
2
votes
2
replies
1.2k
views
Using microarray re-annotation to combine array and Chip-Seq data
re-annotation affymetrix microarrays chip-seq affymetrix mouse gene arrays
5.5 years ago 2323982403 ▴ 60
2
votes
2
replies
1.3k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 4.7 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
2
votes
1
reply
944
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw chip-seq
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ★ 4.1k
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by ▴ 20
1
vote
4
replies
902
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
1
vote
1
reply
830
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 4.5 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
1
vote
4
replies
1.3k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
1
vote
1
reply
931
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by ▴ 20
1
vote
2
replies
1.6k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.6 years ago by 16k • written 6.6 years ago by • 0
1
vote
1
reply
2.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
6.4 years ago chunhong.liu07 ▴ 10
1
vote
5
replies
2.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 3.1 years ago by • 0 • written 6.6 years ago by ▴ 40
1
vote
2
replies
943
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
21 months ago etiennedanis • 0
1
vote
18
replies
3.2k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
0
votes
1
reply
2.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
8.5 years ago eli7javasky • 0
0
votes
2
replies
1.2k
views
Differential ChIP-seq with csaw: How to normalise counts on repetitive regions (telomers)?
csaw histone chip-seq chip-seq
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
0
votes
0
replies
1.2k
views
ChIPQC: Error in names(res) <- nms
ChIPQC chip-seq
6.4 years ago nbkingsley • 0
0
votes
5
replies
1.4k
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 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
0
votes
1
reply
1.3k
views
News: Course Announcement: Use R / Bioconductor for Sequence Analysis (Intermediate Course)
Course RNA-Seq Chip-seq Parallel News
9.2 years ago Martin Morgan 25k
0
votes
7
replies
2.2k
views
Compute average score across multiple bed files
chip-seq granges R bed files
updated 5.8 years ago by • 0 • written 5.8 years ago by • 0
0
votes
2
replies
1.0k
views
csaw normalization and library size
chip-seq normalization
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 260
0
votes
0
replies
912
views
How to properly use and understand chip-seq analysis with DiffBind ?
diffbind chip-seq R
5.6 years ago pierre.marin • 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 260
0
votes
3
replies
859
views
normalization of ChIP-seq data
normalization chip-seq
5.5 years ago Bogdan ▴ 670
0
votes
0
replies
882
views
Recommendation for visualizing ChIP-qPCR data?
R chip-seq histone chip-seq ggbio
5.4 years ago Ramiro Magno ▴ 100
0
votes
6
replies
1.7k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 13 months ago by • 0 • written 23 months ago by ▴ 670
0
votes
1
reply
2.7k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
0
votes
0
replies
1.5k
views
Job: Senior/Junior Bioinformatician - University of Massachusetts Medical School
single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job
4.8 years ago • updated 4.7 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
1.3k
views
HOMER error: Where is the file?
HOMER chip-seq
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
0
votes
0
replies
745
views
Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
4.2 years ago Johannes Rainer ★ 2.0k
0
votes
0
replies
701
views
ChIPQC cross-coverage plot
chipqc chip-seq
4.0 years ago tuteja.reetu • 0
0
votes
1
reply
1.3k
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 3.9 years ago by ★ 5.2k • written 4.0 years ago by ▴ 10
0
votes
1
reply
509
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 3.9 years ago by ★ 5.2k • written 4.0 years ago by ▴ 10
0
votes
2
replies
1.9k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 8.2 years ago by ▴ 110 • written 9.3 years ago by • 0
0
votes
2
replies
1.1k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
0
votes
6
replies
1.8k
views
Normalization - DESeq2 for Differential Binding using ChIP-seq data
deseq2 chip-seq Differential binding
7.9 years ago p2016k • 0
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
3
replies
4.0k
views
DiffBind Analysis with more than 2 samples?
diffbind chip-seq
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by • 0
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
0
votes
1
reply
1.0k
views
DiffBind: Different results with different chromosome names
diffbind chip-seq
updated 7.7 years ago by ★ 5.2k • written 7.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Awards • All
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Locations • All
UPF, Barcelona, Spain, just now
France, 2 minutes ago
United States, 7 minutes ago
United States, 9 minutes ago
United States, 17 minutes ago
Traffic: 811 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