Showing : ATACSeq • reset
8
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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
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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
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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
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8
replies
987
views
Help with error install csaw
ChIPSeq ATACSeq
written 12 months ago by • 0
0
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7
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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
0
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7
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613
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 6 weeks ago by ▴ 10 • written 4 months ago by • 0
4
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6
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885
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
12 months ago Chris • 0
3
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5
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824
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How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by 65k • written 12 months ago by • 0
2
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5
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4.3k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 20 months ago by ▴ 20 • written 2.5 years ago by ▴ 20
2
votes
5
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3.2k
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
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5
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1.7k
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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
1
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4
replies
1.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.8 years ago sh.kazempour94 ▴ 10
2
votes
4
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1.4k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.5 years ago by ★ 5.1k • written 5.6 years ago by ▴ 10
0
votes
4
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1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.6 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
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4
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1.3k
views
DiffBind
ATACSeq DiFFBind
3.0 years ago • updated 2.9 years ago Riba Michela ▴ 90
2
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4
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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 3.1 years ago by • 0
1
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3
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1.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 4 months ago by • 0 • written 23 months ago by • 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
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3
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1.4k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 2.7 years ago by ▴ 80 • written 2.7 years ago by • 0
2
votes
3
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928
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
24 months ago • updated 23 months ago bers.anthrope • 0
1
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2
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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
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2
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1.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 7 months ago by • 0 • written 19 months ago by • 0
0
votes
2
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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
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2
replies
9.1k
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
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2
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782
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 8 months ago by ★ 1.6k • written 8 months ago by • 0
0
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2
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1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.0 years ago tangming2005 ▴ 190
0
votes
1
reply
538
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
2
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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
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
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
640
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
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
276
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
12 weeks ago isaromero8888 • 0
0
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0
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379
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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0
replies
218
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 weeks ago Jawahar • 0
0
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0
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232
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
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0
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558
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.1 years ago hyjforesight • 0
0
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0
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700
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
0
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0
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76
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
20 days ago Pierre Lindenbaum ▴ 10
0
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0
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15
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 hours ago lonn • 0
0
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0
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544
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
41 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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