Showing : ATACSeq • reset
8
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13
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2.7k
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Help with Error in DiffBind
DiffBind ATACSeq
13 months ago • updated 12 months ago Chris • 0
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
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989
views
Help with error install csaw
ChIPSeq ATACSeq
written 12 months ago by • 0
4
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6
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886
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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826
views
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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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
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
2
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5
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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
2
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1
reply
1.5k
views
DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by ★ 5.1k • written 13 months ago by • 0
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
2
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3
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930
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DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
24 months ago • updated 23 months ago bers.anthrope • 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
1
vote
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
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
1
vote
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
1
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5
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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
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
1
vote
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
1
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2
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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
1
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4
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1.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.8 years ago sh.kazempour94 ▴ 10
0
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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
0
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0
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232
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 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
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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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4
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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
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0
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26
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
1 day ago lonn • 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
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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
0
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7
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616
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 6 weeks ago by ▴ 10 • written 4 months ago by • 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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1
reply
538
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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219
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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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
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2
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783
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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0
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380
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
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545
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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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
0
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1
reply
278
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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558
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.1 years ago hyjforesight • 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
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0
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77
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
21 days ago Pierre Lindenbaum ▴ 10
41 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by Michael Love 41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Answer: covariate with negative and positive values by Michael Love 41k
Not a problem. However, if the values are very large (eg 1e6) or very small (eg 1e-6), it's a good idea to center and scale the variable…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist by Sherin • 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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