Showing : atacseq • reset
0
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4
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203
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
10 days ago • updated 7 days ago lonn • 0
0
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0
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87
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
4 weeks ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
291
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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237
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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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0
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249
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
0
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7
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642
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 8 weeks ago by ▴ 10 • written 5 months ago by • 0
0
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0
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395
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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2
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807
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
4
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6
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921
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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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858
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How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by 65k • written 13 months ago by • 0
5
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8
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1.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by • 0
8
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13
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2.8k
views
Help with Error in DiffBind
DiffBind ATACSeq
13 months ago Chris • 0
2
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1
reply
1.5k
views
DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by ★ 5.2k • written 13 months ago by • 0
0
votes
1
reply
651
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 14 months ago by ★ 5.2k • written 15 months ago by • 0
0
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1
reply
553
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
0
votes
0
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562
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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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
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0
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710
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
0
votes
1
reply
1.3k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 22 months ago by ★ 5.2k • written 22 months ago by • 0
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 4 months ago by • 0 • written 24 months ago by • 0
2
votes
3
replies
955
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.0 years ago • updated 23 months ago bers.anthrope • 0
0
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0
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575
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.1 years ago hyjforesight • 0
2
votes
5
replies
4.4k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 20 months ago by ▴ 20 • written 2.6 years ago by ▴ 20
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 20 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
5
votes
8
replies
2.2k
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
1
vote
4
replies
1.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.9 years ago • updated 2.8 years ago sh.kazempour94 ▴ 10
2
votes
5
replies
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 ★ 5.2k
0
votes
4
replies
1.3k
views
DiffBind
ATACSeq DiFFBind
3.0 years ago • updated 2.9 years ago Riba Michela ▴ 90
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 3.1 years ago by 65k • written 3.1 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
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
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.5 years ago by ★ 5.2k • written 3.5 years ago by ▴ 70
0
votes
4
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1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
1
vote
2
replies
9.2k
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
votes
7
replies
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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2
replies
1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.0 years ago tangming2005 ▴ 190
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.1 years ago by ★ 5.2k • written 5.1 years ago by ▴ 10
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 5.1 years ago by 41k • written 5.1 years ago by • 0
2
votes
4
replies
1.4k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
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
41 results • Page 1 of 1
Recent ...
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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