Showing : ATACseq • reset
0
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4
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2.0k
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DiffBind can't find a DAR
dar ATACSeq DiffBind
21 days ago • updated 10 days ago Mengjun • 0
0
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0
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88
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
26 days ago • updated 21 days ago info ▴ 10
0
votes
1
reply
674
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
0
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0
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253
views
diffbind covariates
DiffBind ATACSeq
updated 6 months ago by 43k • written 6 months ago by ▴ 220
2
votes
5
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902
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
7 months ago ronin • 0
0
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0
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711
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
11 months ago Raghad • 0
0
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4
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702
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
12 months ago lonn • 0
0
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0
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456
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
13 months ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
787
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
15 months ago isaromero8888 • 0
0
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0
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793
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
15 months ago Jawahar • 0
0
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0
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546
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
16 months ago inna.gur • 0
0
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7
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1.4k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 14 months ago by ▴ 10 • written 17 months ago by • 0
0
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0
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769
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
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1.7k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 21 months ago by ★ 1.6k • written 21 months ago by • 0
4
votes
6
replies
1.4k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.0 years ago Chris ▴ 20
5
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8
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1.6k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.1 years ago by ▴ 20
3
votes
5
replies
1.3k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.0 years ago by 68k • written 2.1 years ago by ▴ 20
8
votes
13
replies
4.8k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.1 years ago Chris ▴ 20
2
votes
1
reply
3.8k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by ▴ 20
0
votes
1
reply
985
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
1
reply
865
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by • 0
0
votes
0
replies
952
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.4 years ago gogniu • 0
0
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2
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1.9k
views
long computing time for TSS enrichment score
ATACSeq
updated 20 months ago by • 0 • written 2.7 years ago by • 0
0
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0
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979
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.8 years ago Sebastian Lewandowski • 0
0
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1
reply
1.9k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.8 years ago by ★ 5.2k • written 2.9 years ago by • 0
2
votes
3
replies
1.3k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.0 years ago • updated 2.9 years ago bers.anthrope ▴ 10
1
vote
3
replies
2.1k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 17 months ago by • 0 • written 3.0 years ago by • 0
0
votes
0
replies
854
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.1 years ago hyjforesight • 0
2
votes
5
replies
6.3k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.7 years ago by ▴ 20 • written 3.6 years ago by ▴ 20
0
votes
3
replies
1.5k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.7 years ago by ★ 5.2k • written 3.6 years ago by ▴ 40
1
vote
3
replies
2.2k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.8 years ago by ▴ 80 • written 3.8 years ago by • 0
5
votes
8
replies
3.0k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.9 years ago by ▴ 20 • written 3.8 years ago by ▴ 30
1
vote
4
replies
2.0k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.9 years ago sh.kazempour94 ▴ 10
2
votes
5
replies
5.1k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.4 years ago by • 0 • written 3.9 years ago by ★ 5.2k
0
votes
4
replies
1.9k
views
DiffBind
ATACSeq DiFFBind
4.0 years ago • updated 3.9 years ago Riba Michela ▴ 90
1
vote
5
replies
2.3k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by • 0
1
vote
1
reply
2.0k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.5 years ago by ★ 5.2k
1
vote
10
replies
3.5k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.5 years ago by ★ 5.2k • written 4.5 years ago by ▴ 70
0
votes
4
replies
2.6k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by • 0
1
vote
2
replies
13k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by • 0
0
votes
7
replies
2.3k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.9 years ago by ★ 13k • written 5.9 years ago by • 0
0
votes
2
replies
1.6k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.0 years ago tangming2005 ▴ 200
2
votes
1
reply
1.8k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
1
vote
2
replies
2.4k
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 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
4
replies
1.8k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.6k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 30
47 results • Page 1 of 1
Recent ...
Replies
Comment: Module membership vs gene significance result and Modules-trait relationships re by Vinaya • 0
Hi. I am having the same issue, and haven't found a solution still.
Comment: Feature Counts - potential bug with outfile.jcounts by Tom • 0
[Penistone Locksmith][1] I think that would be a great idea; a novel junction to annotated junction proximity output column. So if the nove…
Comment: Filtering after DESeq by caroline.zanchi • 0
I am going to try this right now, thanks !
Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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