Showing : ATACSeq • reset
8
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13
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2.9k
views
Help with Error in DiffBind
DiffBind ATACSeq
14 months ago • updated 13 months ago Chris ▴ 10
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
5
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8
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1.1k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by ▴ 10
4
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6
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950
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
13 months ago Chris ▴ 10
3
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5
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874
views
How to annotate genes from results of DiffBind
ATACSeq
updated 13 months ago by 65k • written 13 months ago by ▴ 10
2
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1
reply
1.4k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.1 years ago by ★ 5.2k • written 5.2 years ago by ▴ 10
2
votes
4
replies
1.5k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.6 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
2
votes
5
replies
3.4k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 17 months ago by • 0 • written 3.0 years ago by ★ 5.2k
2
votes
1
reply
1.6k
views
DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by ★ 5.2k • written 14 months ago by ▴ 10
2
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4
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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
2
votes
3
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971
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.1 years ago • updated 24 months ago bers.anthrope • 0
2
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5
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4.5k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 21 months ago by ▴ 20 • written 2.6 years ago by ▴ 20
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
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
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
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 3.2 years ago by 65k • written 3.2 years ago by • 0
1
vote
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.5 years ago by ★ 5.2k • written 3.6 years ago by ▴ 70
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 42k • written 5.2 years ago by • 0
1
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2
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9.3k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.8 years ago by ★ 1.3k • written 3.8 years ago by • 0
1
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4
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1.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.9 years ago sh.kazempour94 ▴ 10
0
votes
2
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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
0
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0
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278
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 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
votes
7
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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
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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
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261
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
29 days ago • updated 26 days ago lonn • 0
0
votes
1
reply
666
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 15 months ago by ★ 5.2k • written 15 months ago by • 0
0
votes
4
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1.3k
views
DiffBind
ATACSeq DiFFBind
3.1 years ago • updated 3.0 years ago Riba Michela ▴ 90
0
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7
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680
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 10 weeks ago by ▴ 10 • written 5 months ago by • 0
0
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0
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729
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
22 months ago Sebastian Lewandowski • 0
0
votes
1
reply
575
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 16 months ago by ★ 1.3k • written 16 months ago by • 0
0
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0
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266
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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1
reply
1.4k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 22 months ago by ★ 5.2k • written 23 months ago by • 0
0
votes
2
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873
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
0
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0
replies
426
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 65k • written 7 months ago by • 0
0
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0
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587
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
18 months ago gogniu • 0
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 21 months ago by ★ 5.2k • written 2.6 years ago by ▴ 30
0
votes
1
reply
324
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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601
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.2 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 8 months ago by • 0 • written 20 months ago by • 0
0
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0
replies
109
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
41 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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