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
1
vote
10
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2.4k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.5 years ago by ★ 5.2k • written 3.6 years ago by ▴ 70
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
0
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7
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683
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 11 weeks ago by ▴ 10 • written 5 months ago by • 0
0
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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
4
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6
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951
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
13 months ago Chris ▴ 10
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
3
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5
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876
views
How to annotate genes from results of DiffBind
ATACSeq
updated 13 months ago by 65k • written 13 months ago by ▴ 10
2
votes
5
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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
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
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
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
0
votes
4
replies
2.0k
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
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 28 days ago lonn • 0
0
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4
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1.3k
views
DiffBind
ATACSeq DiFFBind
3.1 years ago • updated 3.0 years ago Riba Michela ▴ 90
1
vote
4
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1.6k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.9 years ago sh.kazempour94 ▴ 10
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
2
votes
3
replies
972
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.1 years ago • updated 24 months ago bers.anthrope • 0
0
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3
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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
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
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
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
1
vote
2
replies
9.4k
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
0
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2
replies
1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.0 years ago tangming2005 ▴ 190
0
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2
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875
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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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
2
votes
1
reply
1.4k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by ▴ 10
0
votes
1
reply
327
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
votes
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
1
reply
669
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
2
votes
1
reply
1.7k
views
DiffBind on ATAC seq data
ATACSeq
updated 14 months ago by ★ 5.2k • written 14 months ago by ▴ 10
0
votes
1
reply
576
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 16 months ago by ★ 1.3k • written 16 months ago by • 0
1
vote
1
reply
1.5k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.6 years ago by ★ 5.2k
0
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0
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732
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
22 months ago Sebastian Lewandowski • 0
0
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0
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109
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
0
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0
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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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590
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
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0
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280
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
0
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0
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603
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.2 years ago hyjforesight • 0
0
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0
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267
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
41 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
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