Showing : ATACseq • reset
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2.2k
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DiffBind can't find a DAR
dar ATACSeq DiffBind
5 months ago • updated 4 months ago Mengjun • 0
0
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0
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265
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
5 months ago info ▴ 10
0
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1
reply
847
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
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0
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331
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diffbind covariates
DiffBind ATACSeq
updated 10 months ago by 43k • written 10 months ago by ▴ 220
2
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5
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1.1k
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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
11 months ago ronin • 0
0
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0
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846
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
15 months ago Raghad • 0
0
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4
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877
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
17 months ago • updated 16 months ago lonn • 0
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0
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551
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
17 months ago Pierre Lindenbaum ▴ 10
0
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1
reply
914
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
19 months ago isaromero8888 • 0
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0
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893
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
19 months ago Jawahar • 0
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0
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625
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
20 months ago inna.gur • 0
0
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7
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1.6k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 18 months ago by ▴ 10 • written 21 months ago by • 0
0
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0
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912
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 23 months ago by 68k • written 23 months ago by • 0
0
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2
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1.9k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by • 0
4
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6
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1.6k
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Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.4 years ago Chris ▴ 20
5
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8
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1.8k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.5 years ago by ▴ 20
3
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5
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1.5k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 20
8
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13
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5.2k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.5 years ago • updated 2.4 years ago Chris ▴ 20
2
votes
1
reply
4.1k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by ▴ 20
0
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1
reply
1.1k
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
votes
1
reply
972
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.7 years ago by ★ 1.3k • written 2.7 years ago by • 0
0
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0
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1.1k
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.8 years ago gogniu • 0
0
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2
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2.0k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.0 years ago by • 0 • written 3.0 years ago by • 0
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0
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1.1k
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.1 years ago Sebastian Lewandowski • 0
0
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1
reply
2.0k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.2 years ago by ★ 5.2k • written 3.2 years ago by • 0
2
votes
3
replies
1.5k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.4 years ago • updated 3.3 years ago bers.anthrope ▴ 10
1
vote
3
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2.3k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 21 months ago by • 0 • written 3.4 years ago by • 0
0
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0
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927
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.5 years ago hyjforesight • 0
2
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5
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6.7k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.1 years ago by ▴ 20 • written 3.9 years ago by ▴ 20
0
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3
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1.7k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.1 years ago by ★ 5.2k • written 3.9 years ago by ▴ 40
1
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3
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2.3k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.1 years ago by ▴ 80 • written 4.1 years ago by • 0
5
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8
replies
3.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.3 years ago by ▴ 20 • written 4.2 years ago by ▴ 30
1
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4
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2.2k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.2 years ago sh.kazempour94 ▴ 10
2
votes
5
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5.4k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.7 years ago by • 0 • written 4.3 years ago by ★ 5.2k
0
votes
4
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2.0k
views
DiffBind
ATACSeq DiFFBind
4.4 years ago • updated 4.3 years ago Riba Michela ▴ 90
1
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5
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2.5k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
2
votes
4
replies
2.2k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.5 years ago by ★ 5.2k • written 4.5 years ago by • 0
1
vote
1
reply
2.1k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.9 years ago by ★ 5.2k
1
vote
10
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3.8k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.8 years ago by ★ 5.2k • written 4.9 years ago by ▴ 70
0
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4
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2.8k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.0 years ago by ★ 1.3k • written 5.1 years ago by • 0
1
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2
replies
13k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.1 years ago by ★ 1.3k • written 5.1 years ago by • 0
0
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7
replies
2.5k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.2 years ago by ★ 13k • written 6.2 years ago by • 0
0
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2
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1.7k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.3 years ago tangming2005 ▴ 200
2
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1
reply
1.9k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by ▴ 10
1
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2
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2.5k
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 6.5 years ago by 43k • written 6.5 years ago by • 0
2
votes
4
replies
1.9k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.9 years ago by ★ 5.2k • written 7.0 years ago by ▴ 10
0
votes
2
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1.7k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 7.2 years ago by • 0 • written 7.2 years ago by ▴ 30
47 results • Page 1 of 1
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Replies
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Votes
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
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