Showing : ATACSeq • reset
0
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4
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229
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 12 days ago lonn • 0
0
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0
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93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
297
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
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0
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244
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
0
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0
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256
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
0
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7
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652
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 8 weeks ago by ▴ 10 • written 5 months ago by • 0
0
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0
replies
405
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
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2
replies
832
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
4
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6
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926
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
12 months ago Chris • 0
5
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8
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1.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by • 0
3
votes
5
replies
861
views
How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by 65k • written 13 months ago by • 0
8
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13
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2.8k
views
Help with Error in DiffBind
DiffBind ATACSeq
13 months ago Chris • 0
2
votes
1
reply
1.6k
views
DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by ★ 5.2k • written 13 months ago by • 0
0
votes
1
reply
658
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 14 months ago by ★ 5.2k • written 15 months ago by • 0
0
votes
1
reply
560
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
0
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0
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571
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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2
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1.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 8 months ago by • 0 • written 20 months ago by • 0
0
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0
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718
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
0
votes
1
reply
1.3k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 22 months ago by ★ 5.2k • written 22 months ago by • 0
2
votes
3
replies
958
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.0 years ago • updated 23 months ago bers.anthrope • 0
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 5 months ago by • 0 • written 2.0 years ago by • 0
0
votes
0
replies
581
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.1 years ago hyjforesight • 0
2
votes
5
replies
4.4k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 20 months ago by ▴ 20 • written 2.6 years ago by ▴ 20
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 20 months ago by ★ 5.2k • written 2.6 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
5
votes
8
replies
2.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 23 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
1
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4
replies
1.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.9 years ago sh.kazempour94 ▴ 10
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 ★ 5.2k
0
votes
4
replies
1.3k
views
DiffBind
ATACSeq DiFFBind
3.0 years ago Riba Michela ▴ 90
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
1.6k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.2 years ago by ★ 5.2k • written 3.2 years 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 ★ 5.2k
1
vote
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.5 years ago by ★ 5.2k • written 3.5 years ago by ▴ 70
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
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
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.9 years ago by ★ 13k • written 4.9 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
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 ★ 5.2k • written 5.1 years ago by ▴ 10
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 5.2 years ago by 41k • written 5.2 years ago by • 0
2
votes
4
replies
1.4k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
0
votes
2
replies
1.2k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 5.9 years ago by • 0 • written 5.9 years ago by ▴ 30
41 results • Page 1 of 1
Recent ...
Replies
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank" by James W. MacDonald 65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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