Showing : ATACseq • reset
1
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9.3k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.7 years ago by ★ 1.3k • written 3.8 years ago by • 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
2
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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
8
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13
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2.8k
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Help with Error in DiffBind
DiffBind ATACSeq
13 months ago Chris • 0
1
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10
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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
5
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8
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2.2k
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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
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2
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2.0k
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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
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4
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1.9k
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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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7
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1.8k
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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
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5
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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
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1
reply
1.6k
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DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by ★ 5.2k • written 13 months ago by • 0
1
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3
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1.6k
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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
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4
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1.6k
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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
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4
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1.5k
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Binding matrix created by DiffBind
ATACSeq DiffBind
2.9 years ago sh.kazempour94 ▴ 10
1
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1
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1.5k
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News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.5 years ago by ★ 5.2k
1
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3
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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
2
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4
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1.5k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
2
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1
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1.4k
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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
0
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1
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1.3k
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Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 22 months ago by ★ 5.2k • written 22 months ago by • 0
0
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4
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1.3k
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DiffBind
ATACSeq DiFFBind
3.1 years ago • updated 3.0 years ago Riba Michela ▴ 90
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2
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1.2k
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long computing time for TSS enrichment score
ATACSeq
updated 8 months ago by • 0 • written 20 months ago by • 0
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2
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1.2k
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calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.0 years ago tangming2005 ▴ 190
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2
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1.2k
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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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3
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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
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
2
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3
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963
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DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.0 years ago • updated 23 months ago bers.anthrope • 0
4
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6
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939
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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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870
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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
0
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2
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853
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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
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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
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7
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666
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 9 weeks ago by ▴ 10 • written 5 months ago by • 0
0
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1
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662
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
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0
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589
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[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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582
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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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1
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569
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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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413
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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1
reply
310
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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264
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
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0
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253
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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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4
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245
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
22 days ago • updated 20 days ago lonn • 0
0
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0
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
6 weeks ago Pierre Lindenbaum ▴ 10
41 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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