Showing : ATACSeq • reset
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
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0
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205
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diffbind covariates
DiffBind ATACSeq
updated 4 months ago by 43k • written 4 months ago by ▴ 220
2
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5
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818
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Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
5 months ago ronin • 0
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0
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596
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
9 months ago Raghad • 0
0
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4
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649
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
10 months ago lonn • 0
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409
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
11 months ago Pierre Lindenbaum ▴ 10
0
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1
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726
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
13 months ago isaromero8888 • 0
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0
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713
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
13 months ago Jawahar • 0
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0
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507
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
14 months ago inna.gur • 0
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7
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1.3k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 12 months ago by ▴ 10 • written 15 months ago by • 0
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0
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725
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 17 months ago by 68k • written 17 months ago by • 0
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2
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1.6k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 19 months ago by ★ 1.6k • written 19 months ago by • 0
4
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6
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1.4k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
22 months ago Chris ▴ 20
5
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8
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1.5k
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Help with error install csaw
ChIPSeq ATACSeq
written 23 months ago by ▴ 20
3
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5
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1.3k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 22 months ago by 68k • written 23 months ago by ▴ 20
8
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13
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4.4k
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Help with Error in DiffBind
DiffBind ATACSeq
23 months ago Chris ▴ 20
2
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1
reply
3.5k
views
DiffBind on ATAC seq data
ATACSeq
updated 23 months ago by ★ 5.2k • written 23 months ago by ▴ 20
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1
reply
932
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
0
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1
reply
822
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by • 0
0
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0
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896
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.3 years ago gogniu • 0
0
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2
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1.8k
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long computing time for TSS enrichment score
ATACSeq
updated 18 months ago by • 0 • written 2.5 years ago by • 0
0
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0
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949
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.6 years ago Sebastian Lewandowski • 0
0
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1
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1.8k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
2
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3
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1.3k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.9 years ago • updated 2.8 years ago bers.anthrope ▴ 10
1
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3
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2.1k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 15 months ago by • 0 • written 2.8 years ago by • 0
0
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0
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821
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.0 years ago hyjforesight • 0
2
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5
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6.0k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.6 years ago by ▴ 20 • written 3.4 years ago by ▴ 20
0
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3
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1.5k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.5 years ago by ★ 5.2k • written 3.4 years ago by ▴ 40
1
vote
3
replies
2.1k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.6 years ago by ▴ 80 • written 3.6 years ago by • 0
5
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8
replies
2.8k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.7 years ago by ▴ 20 • written 3.6 years ago by ▴ 30
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4
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2.0k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.7 years ago sh.kazempour94 ▴ 10
2
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5
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4.8k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.2 years ago by • 0 • written 3.8 years ago by ★ 5.2k
0
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4
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1.8k
views
DiffBind
ATACSeq DiFFBind
3.9 years ago • updated 3.8 years ago Riba Michela ▴ 90
1
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5
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2.3k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.9 years ago by 68k • written 4.0 years ago by • 0
2
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4
replies
2.0k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by • 0
1
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1
reply
1.9k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.3 years ago by ★ 5.2k
1
vote
10
replies
3.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.3 years ago by ★ 5.2k • written 4.4 years ago by ▴ 70
0
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4
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2.5k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by • 0
1
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2
replies
12k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by • 0
0
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7
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2.2k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.7 years ago by ★ 13k • written 5.7 years ago by • 0
0
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2
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1.5k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.8 years ago tangming2005 ▴ 200
2
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1
reply
1.7k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.9 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
1
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2
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2.3k
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 6.0 years ago by 43k • written 6.0 years ago by • 0
2
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4
replies
1.8k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.4 years ago by ★ 5.2k • written 6.5 years ago by ▴ 10
0
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2
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1.5k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.7 years ago by • 0 • written 6.7 years ago by ▴ 30
45 results • Page 1 of 1
Recent ...
Replies
Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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