Showing : ATACSeq • reset
8
votes
13
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2.7k
views
Help with Error in DiffBind
DiffBind ATACSeq
13 months ago • updated 12 months ago Chris • 0
1
vote
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.4 years ago by ★ 5.1k • written 3.5 years ago by ▴ 70
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 22 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
5
votes
8
replies
999
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by • 0
0
votes
7
replies
626
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 7 weeks ago by ▴ 10 • written 4 months ago by • 0
0
votes
7
replies
1.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.8 years ago by ★ 13k • written 4.8 years ago by • 0
4
votes
6
replies
897
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
12 months ago Chris • 0
2
votes
5
replies
4.4k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 20 months ago by ▴ 20 • written 2.5 years ago by ▴ 20
3
votes
5
replies
837
views
How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by 65k • written 12 months ago by • 0
2
votes
5
replies
3.3k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 16 months ago by • 0 • written 2.9 years ago by ★ 5.1k
1
vote
5
replies
1.7k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
2
votes
4
replies
1.5k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.1 years ago by ★ 5.1k • written 3.2 years ago by • 0
2
votes
4
replies
1.4k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.6 years ago by ★ 5.1k • written 5.6 years ago by ▴ 10
0
votes
4
replies
1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
votes
4
replies
177
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
5 days ago • updated 3 days ago lonn • 0
0
votes
4
replies
1.3k
views
DiffBind
ATACSeq DiFFBind
3.0 years ago • updated 2.9 years ago Riba Michela ▴ 90
1
vote
4
replies
1.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.9 years ago • updated 2.8 years ago sh.kazempour94 ▴ 10
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 4 months ago by • 0 • written 24 months ago by • 0
2
votes
3
replies
942
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.0 years ago • updated 23 months ago bers.anthrope • 0
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 20 months ago by ★ 5.1k • written 2.5 years ago by ▴ 30
1
vote
3
replies
1.5k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 2.8 years ago by ▴ 80 • written 2.8 years ago by • 0
1
vote
2
replies
2.0k
views
DeSEQ2- What is the difference between Gene Clustering and using LRT for Time Series experiment WITHOUT treatments
deseq2 Time Series Gene Clustering LRT ATACseq
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
0
votes
2
replies
1.1k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 5.8 years ago by • 0 • written 5.9 years ago by ▴ 30
1
vote
2
replies
9.2k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
votes
2
replies
1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.0 years ago tangming2005 ▴ 190
0
votes
2
replies
791
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
0
votes
2
replies
1.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 8 months ago by • 0 • written 20 months ago by • 0
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.1 years ago by ★ 5.1k • written 5.1 years ago by ▴ 10
0
votes
1
reply
285
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
12 weeks ago isaromero8888 • 0
0
votes
1
reply
1.3k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 21 months ago by ★ 5.1k • written 22 months ago by • 0
0
votes
1
reply
646
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 14 months ago by ★ 5.1k • written 14 months ago by • 0
2
votes
1
reply
1.5k
views
DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by ★ 5.1k • written 13 months ago by • 0
0
votes
1
reply
546
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
1
vote
1
reply
1.5k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.5 years ago by ★ 5.1k
0
votes
0
replies
705
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
0
votes
0
replies
83
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
25 days ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
385
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
0
votes
0
replies
553
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
17 months ago gogniu • 0
0
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0
replies
239
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
votes
0
replies
567
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.1 years ago hyjforesight • 0
0
votes
0
replies
227
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
41 results • Page 1 of 1
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Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Comment: Limma design with continuous and categorical covariates by hortense96 • 0
Hello, I'm trying to do a differential methylation analysis with the Limma package and was wondering if you had any suggestions on how to …
Answer: minfi::read.metharray.exp by Basti ▴ 770
Could you show `list.files("~/Users/clarachretienneau/Desktop/clock epigenetic/PJ1209132_ScanData")` ? There may be a problem related to th…
Comment: DESeq2 - dispersion estimation when there is none by WardDeb • 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by Gayatri • 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Votes
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
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