Showing : atacseq • reset
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
9 weeks ago Raghad • 0
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4
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383
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
3 months ago lonn • 0
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194
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
4 months ago Pierre Lindenbaum ▴ 10
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1
reply
408
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
6 months ago isaromero8888 • 0
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0
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364
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
6 months ago Jawahar • 0
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330
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
7 months ago inna.gur • 0
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7
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856
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 4 months ago by ▴ 10 • written 8 months ago by • 0
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0
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503
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 9 months ago by 66k • written 9 months ago by • 0
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2
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1.1k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 12 months ago by ★ 1.6k • written 12 months ago by • 0
4
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6
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1.1k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
15 months ago Chris ▴ 20
5
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8
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1.2k
views
Help with error install csaw
ChIPSeq ATACSeq
written 16 months ago by ▴ 20
3
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5
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960
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How to annotate genes from results of DiffBind
ATACSeq
updated 15 months ago by 66k • written 16 months ago by ▴ 20
8
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13
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3.2k
views
Help with Error in DiffBind
DiffBind ATACSeq
16 months ago Chris ▴ 20
2
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1
reply
2.1k
views
DiffBind on ATAC seq data
ATACSeq
updated 16 months ago by ★ 5.2k • written 16 months ago by ▴ 20
0
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1
reply
725
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 17 months ago by ★ 5.2k • written 18 months ago by • 0
0
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1
reply
659
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 18 months ago by ★ 1.3k • written 18 months ago by • 0
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0
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673
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
20 months ago gogniu • 0
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2
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1.4k
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long computing time for TSS enrichment score
ATACSeq
updated 11 months ago by • 0 • written 23 months ago by • 0
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0
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786
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.0 years ago Sebastian Lewandowski • 0
0
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1
reply
1.5k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
2
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3
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1.0k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.3 years ago • updated 2.2 years ago bers.anthrope • 0
1
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3
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1.7k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 7 months ago by • 0 • written 2.2 years ago by • 0
0
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0
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677
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.4 years ago hyjforesight • 0
2
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5
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4.8k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 23 months ago by ▴ 20 • written 2.8 years ago by ▴ 20
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3
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1.2k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 23 months ago by ★ 5.2k • written 2.8 years ago by ▴ 30
1
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3
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1.7k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.0 years ago by ▴ 80 • written 3.0 years ago by • 0
5
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8
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2.4k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.1 years ago by ▴ 20 • written 3.0 years ago by ▴ 30
1
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4
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1.7k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.1 years ago sh.kazempour94 ▴ 10
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5
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3.8k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 19 months ago by • 0 • written 3.2 years ago by ★ 5.2k
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4
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1.4k
views
DiffBind
ATACSeq DiFFBind
3.3 years ago • updated 3.2 years ago Riba Michela ▴ 90
1
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5
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1.9k
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How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.3 years ago by 66k • written 3.4 years ago by • 0
2
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4
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1.7k
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DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.4 years ago by ★ 5.2k • written 3.4 years ago by • 0
1
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1
reply
1.6k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.7 years ago by ★ 5.2k
1
vote
10
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2.6k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.7 years ago by ★ 5.2k • written 3.8 years ago by ▴ 70
0
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4
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2.1k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.9 years ago by ★ 1.3k • written 3.9 years ago by • 0
1
vote
2
replies
9.9k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.9 years ago by ★ 1.3k • written 4.0 years ago by • 0
0
votes
7
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1.9k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
0
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2
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1.3k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.2 years ago tangming2005 ▴ 190
2
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1
reply
1.5k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.3 years ago by ★ 5.2k • written 5.4 years ago by ▴ 10
1
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2
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2.1k
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 5.4 years ago by 42k • written 5.4 years ago by • 0
2
votes
4
replies
1.6k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.8 years ago by ★ 5.2k • written 5.9 years ago by ▴ 10
0
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2
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1.2k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.1 years ago by • 0 • written 6.1 years ago by ▴ 30
42 results • Page 1 of 1
Recent ...
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Answer: Validity of SingleR with very small bulk RNAseq reference by ATpoint ★ 4.2k
The vignette data are "large" because it is single-cell data and each cell is considered in this case a "replicate". With bulk RNA-seq you …
Answer: Plot PCA with ellipses using ggplot by ATpoint ★ 4.2k
This is rather a ggplot than DESeq2 question, please see for example https://stackoverflow.com/questions/49931681/error-too-few-points-to-c…
Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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