Showing : ATACseq • reset
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28
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
1 day ago jfmay • 0
0
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0
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158
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 weeks ago by 64k • written 7 weeks ago by • 0
0
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2
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471
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 4 months ago by ★ 1.6k • written 4 months ago by • 0
4
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6
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672
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Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
7 months ago Chris • 0
5
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8
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719
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Help with error install csaw
ChIPSeq ATACSeq
updated 8 months ago by • 0 • written 8 months ago by • 0
3
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5
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651
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How to annotate genes from results of DiffBind
ATACSeq
updated 7 months ago by 64k • written 8 months ago by • 0
8
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13
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1.8k
views
Help with Error in DiffBind
DiffBind ATACSeq
8 months ago Chris • 0
1
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1
reply
679
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DiffBind on ATAC seq data
ATACSeq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
0
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1
reply
429
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 9 months ago by ★ 5.1k • written 10 months ago by • 0
0
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1
reply
403
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 10 months ago by ★ 1.3k • written 10 months ago by • 0
0
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0
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373
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
12 months ago gogniu • 0
0
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2
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779
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long computing time for TSS enrichment score
ATACSeq
updated 3 months ago by • 0 • written 15 months ago by • 0
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0
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545
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
16 months ago Sebastian Lewandowski • 0
0
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1
reply
998
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Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 17 months ago by ★ 5.1k • written 17 months ago by • 0
2
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3
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787
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DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
19 months ago • updated 18 months ago bers.anthrope • 0
1
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2
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1.2k
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regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
19 months ago zgraytho88 • 0
0
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0
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443
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
20 months ago hyjforesight • 0
2
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5
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3.7k
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using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 15 months ago by ▴ 20 • written 2.2 years ago by ▴ 20
0
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3
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930
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 15 months ago by ★ 5.1k • written 2.2 years ago by ▴ 30
1
vote
3
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1.2k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 2.4 years ago by ▴ 80 • written 2.4 years ago by • 0
5
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8
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1.8k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 17 months ago by ▴ 20 • written 2.4 years ago by ▴ 30
1
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4
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1.3k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.5 years ago • updated 2.4 years ago sh.kazempour94 ▴ 10
2
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5
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2.7k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 11 months ago by • 0 • written 2.5 years ago by ★ 5.1k
0
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4
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1.1k
views
DiffBind
ATACSeq DiFFBind
2.6 years ago • updated 2.5 years ago Riba Michela ▴ 90
1
vote
5
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1.5k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 2.7 years ago by 64k • written 2.7 years ago by • 0
2
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4
replies
1.3k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 2.8 years ago by ★ 5.1k • written 2.8 years ago by • 0
1
vote
1
reply
1.4k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.1 years ago by ★ 5.1k
1
vote
10
replies
1.8k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.1 years ago by ★ 5.1k • written 3.1 years ago by ▴ 70
0
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4
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1.7k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.3 years ago by ★ 1.3k • written 3.3 years ago by • 0
1
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2
replies
7.8k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.3 years ago by ★ 1.3k • written 3.3 years ago by • 0
0
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7
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1.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.4 years ago by 13k • written 4.4 years ago by • 0
0
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2
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1.0k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
4.6 years ago tangming2005 ▴ 190
2
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1
reply
1.1k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 4.7 years ago by ★ 5.1k • written 4.7 years ago by ▴ 10
1
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2
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1.8k
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 4.7 years ago by 41k • written 4.7 years ago by • 0
2
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4
replies
1.3k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.2 years ago by ★ 5.1k • written 5.2 years ago by ▴ 10
0
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2
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1.0k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 5.5 years ago by • 0 • written 5.5 years ago by ▴ 30
36 results • Page 1 of 1
Recent ...
Replies
Answer: Obtaining rsIDs with ENSG and variant ID information by Robert Castelo ★ 3.0k
You should first and foremost find out what was the human reference genome version from which your dataset was derived. Assuming this was G…
Comment: DESeq2 - groups with biological replicates from the same patient by James W. MacDonald 64k
If by clustering you mean there might be a within-subject correlation, then yes it's a possibility. But you cannot control for that using a…
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Mike Smith ★ 6.2k
If we hover over the tiny little red icon next to the Linux build report, we can see that the source package isn't being distributed becaus…
Comment: ClusterProfiler - enrichKEGG on specific pathways by EvaLan • 0
Hey bekah, I wonder if you have found the solution to solve this issue? Best wishes, EvaLan
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Gordon Smyth 48k
That's a good question. On the DMRcate landing page, one can see that the "Source package" file is missing, meaning that installation in Un…
Votes
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Answer: trying to add SingleR label to Seurat Object fails
Comment: DESeq2 - groups with biological replicates from the same patient
Answer: EdgeR: Exact test and glmQLFTest produce very different results
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