Showing : ATACseq • reset
1
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2.2k
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How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
0
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2
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1.4k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 17 months ago by ★ 1.6k • written 17 months ago by • 0
8
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13
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4.2k
views
Help with Error in DiffBind
DiffBind ATACSeq
22 months ago • updated 21 months ago Chris ▴ 20
1
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2
replies
11k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
5
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8
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1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 21 months ago by ▴ 20
2
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5
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733
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
3 months ago ronin • 0
1
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10
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3.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by ▴ 70
5
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8
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2.7k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.6 years ago by ▴ 20 • written 3.5 years ago by ▴ 30
0
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2
replies
1.4k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 30
0
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7
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1.2k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 10 months ago by ▴ 10 • written 13 months ago by • 0
1
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4
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1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.6 years ago sh.kazempour94 ▴ 10
2
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4
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1.9k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.9 years ago by ★ 5.2k • written 3.9 years ago by • 0
2
votes
4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
1
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2
replies
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 5.9 years ago by 43k • written 5.9 years ago by • 0
2
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1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
0
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4
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2.3k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
2
votes
1
reply
3.1k
views
DiffBind on ATAC seq data
ATACSeq
updated 22 months ago by ★ 5.2k • written 22 months ago by ▴ 20
4
votes
6
replies
1.3k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
21 months ago Chris ▴ 20
0
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1
reply
884
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 23 months ago by ★ 5.2k • written 23 months ago by • 0
0
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4
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1.7k
views
DiffBind
ATACSeq DiFFBind
3.7 years ago Riba Michela ▴ 90
2
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3
replies
1.2k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.7 years ago • updated 2.6 years ago bers.anthrope ▴ 10
0
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1
reply
1.8k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.6 years ago by • 0
1
vote
3
replies
2.0k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.5 years ago by ▴ 80 • written 3.5 years ago by • 0
2
votes
5
replies
5.7k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.4 years ago by ▴ 20 • written 3.3 years ago by ▴ 20
3
votes
5
replies
1.2k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 21 months ago by 67k • written 21 months ago by ▴ 20
0
votes
1
reply
392
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
votes
1
reply
793
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
1
vote
3
replies
2.0k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 13 months ago by • 0 • written 2.7 years ago by • 0
0
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0
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658
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
11 months ago Jawahar • 0
0
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2
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1.4k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.7 years ago tangming2005 ▴ 200
0
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7
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2.1k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.6 years ago by ★ 13k • written 5.6 years ago by • 0
0
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0
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671
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 15 months ago by 67k • written 15 months ago by • 0
0
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0
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152
views
diffbind covariates
DiffBind ATACSeq
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 220
0
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0
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844
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.1 years ago gogniu • 0
0
votes
3
replies
1.4k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.4 years ago by ★ 5.2k • written 3.3 years ago by ▴ 40
0
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0
replies
468
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
12 months ago inna.gur • 0
0
votes
1
reply
644
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
11 months ago isaromero8888 • 0
0
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0
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795
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.8 years ago hyjforesight • 0
0
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2
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1.7k
views
long computing time for TSS enrichment score
ATACSeq
updated 16 months ago by • 0 • written 2.4 years ago by • 0
2
votes
5
replies
4.6k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.1 years ago by • 0 • written 3.6 years ago by ★ 5.2k
0
votes
0
replies
907
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.5 years ago Sebastian Lewandowski • 0
0
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0
replies
362
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
9 months ago Pierre Lindenbaum ▴ 10
0
votes
4
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583
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 months ago • updated 8 months ago lonn • 0
0
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0
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492
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
7 months ago Raghad • 0
1
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1
reply
1.9k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.2 years ago by ★ 5.2k
45 results • Page 1 of 1
Recent ...
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
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