Showing : Chip-Seq • reset
1
vote
18
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3.3k
views
Normalization of chip-seq data in manually specified regions using CSAW
chip-seq TSS TMM csaw
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
3
votes
11
replies
2.4k
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
9
replies
2.9k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
8.7 years ago lindahove ▴ 10
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 3.9 years ago by ▴ 20
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
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
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
0
votes
6
replies
1.7k
views
performing the differential binding in ChIP-seq
ChIP-seq
updated 13 months ago by • 0 • written 24 months ago by ▴ 670
1
vote
5
replies
2.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind dba.count Chip-Seq Differential analysis
updated 3.2 years ago by • 0 • written 6.7 years ago by ▴ 40
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 6.0 years ago by ★ 28k • written 6.0 years ago by • 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 7.9 years ago by • 0
1
vote
4
replies
913
views
in diffbind dba.peakset what is the meaning of minOverlap?
diffbind chip-seq dba.peakset
updated 4.6 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
1
vote
4
replies
1.4k
views
transcriptR ChIP-seq RNA-seq bam Error in mergeNamedAtomicVectors
TranscriptR RNA-seq ChIP-seq
updated 4.5 years ago by 65k • written 4.6 years ago by • 0
4
votes
4
replies
1.6k
views
Strand-aware CSAW analysis
csaw chip-seq clip-seq
9.3 years ago IV ▴ 30
3
votes
4
replies
2.0k
views
Interpretation of cross correlation plot to determine fragment length
csaw chip-seq histone
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
3
votes
4
replies
1.7k
views
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
DiffBind SpikeIn Normalization ChIP-seq csaw
17 months ago • updated 16 months ago spg • 0
0
votes
4
replies
1.4k
views
csaw spike-in normalization
ChIP-seq csaw
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 260
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
0
votes
3
replies
870
views
normalization of ChIP-seq data
normalization chip-seq
5.5 years ago Bogdan ▴ 670
0
votes
3
replies
1.9k
views
Clarification on Normalization Approach in DiffBind's db.analyze()
diffbind chip-seq normalization deseq2 tmm
updated 7.3 years ago by ★ 5.2k • written 7.3 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
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 6.9 years ago by ▴ 10
0
votes
2
replies
1.9k
views
Diffbind plotting on contrasts
diffbind chip-seq
updated 8.3 years ago by ▴ 110 • written 9.3 years ago by • 0
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 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
0
votes
2
replies
1.6k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
3
votes
2
replies
921
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
1
vote
2
replies
1.7k
views
Errors with makeTxDbFromBiomart
chip-seq
updated 6.7 years ago by 16k • written 6.7 years ago by • 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 6.7 years ago by ★ 28k • written 6.7 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
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
1.4k
views
ChIPQC gives Bam file has 297 contigs Error: subscript contains out-of-bounds indices
ChIP-seq ChIPQC QC
updated 4.8 years ago by ▴ 20 • written 5.2 years ago by ▴ 10
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
1
vote
2
replies
969
views
Could it be possible to get an older version of ChIPQC?
ChIPQC ChIP-seq DiffBind Rory_Stark
22 months ago • updated 21 months ago etiennedanis • 0
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
1
reply
515
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
1
reply
758
views
meta-gene profiles
ChIP-seq
updated 2.2 years ago by ▴ 60 • written 2.2 years ago by ▴ 670
0
votes
1
reply
2.4k
views
diffBind - bam not accessible
diffbind chip-seq bam
8.6 years ago eli7javasky • 0
0
votes
1
reply
1.1k
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
1
vote
1
reply
2.2k
views
Importing Chip-Seq Peak MACS2 output (.xls) files into DBA object with Diffbind?
diffbind macs2 chip-seq
6.5 years ago chunhong.liu07 ▴ 10
0
votes
1
reply
1.5k
views
Soggi regionPlot function gave error when import bigwig file with "percentOfRegion" mode
soGGi chip-seq region
updated 6.7 years ago by ▴ 420 • written 6.8 years ago by • 0
2
votes
1
reply
1.2k
views
problem with characters in chromosome names in DiffBind dba
DiffBind ChIP-Seq
updated 9.5 years ago by ★ 5.2k • written 9.5 years ago by ▴ 120
0
votes
1
reply
1.5k
views
Chip-seq peak annotation [Chipseeker]
chipseeker chip-seq annotation Guangchuang
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
1
vote
1
reply
947
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
1
reply
839
views
Diffbind with age as blocking factor
diffbind chip-seq
updated 4.6 years ago by ★ 5.2k • written 4.6 years ago by ▴ 10
2
votes
1
reply
1.0k
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
1
reply
957
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
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
1
reply
2.8k
views
Reading peaks from MACS2 with DiffBind
chip-seq peak calling diffbind
updated 5.0 years ago by ★ 5.2k • written 5.0 years ago by • 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 4.1 years ago by ▴ 10
0
votes
0
replies
753
views
Job: Bolzano, Italy: Post Doc Researcher in bioinformatics of cancer epigenomics
RNA-seq ChIP-seq Job
4.3 years ago Johannes Rainer ★ 2.0k
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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