Showing : atacseq • reset
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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0
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186
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diffbind covariates
DiffBind ATACSeq
updated 3 months ago by 43k • written 3 months ago by ▴ 220
2
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5
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781
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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
4 months ago ronin • 0
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0
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562
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
8 months ago Raghad • 0
0
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4
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619
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
10 months ago • updated 9 months ago lonn • 0
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0
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389
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
10 months ago Pierre Lindenbaum ▴ 10
0
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1
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698
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
12 months ago isaromero8888 • 0
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0
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696
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 months ago Jawahar • 0
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0
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494
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
13 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 11 months ago by ▴ 10 • written 14 months ago by • 0
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0
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708
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 16 months ago by 68k • written 16 months ago by • 0
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2
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1.5k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 18 months ago by ★ 1.6k • written 18 months ago by • 0
4
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6
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1.3k
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 22 months ago by ▴ 20
3
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5
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1.2k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 22 months ago by 68k • written 22 months ago by ▴ 20
8
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13
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4.3k
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Help with Error in DiffBind
DiffBind ATACSeq
23 months ago • updated 22 months ago Chris ▴ 20
2
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1
reply
3.3k
views
DiffBind on ATAC seq data
ATACSeq
updated 23 months ago by ★ 5.2k • written 23 months ago by ▴ 20
0
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1
reply
911
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.0 years ago by ★ 5.2k • written 2.0 years ago by • 0
0
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1
reply
804
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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872
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.2 years ago gogniu • 0
0
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2
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1.8k
views
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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934
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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 2.6 years ago by ★ 5.2k • written 2.7 years ago by • 0
2
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3
replies
1.3k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.8 years ago • updated 2.7 years ago bers.anthrope ▴ 10
1
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3
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2.0k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 14 months ago by • 0 • written 2.8 years ago by • 0
0
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0
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809
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.9 years ago hyjforesight • 0
2
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5
replies
5.9k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.5 years ago by ▴ 20 • written 3.4 years ago by ▴ 20
0
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3
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1.4k
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package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.5 years ago by ★ 5.2k • written 3.4 years ago by ▴ 40
1
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3
replies
2.0k
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
votes
8
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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
1
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4
replies
1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.7 years ago • updated 3.6 years ago sh.kazempour94 ▴ 10
2
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5
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4.7k
views
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 3.7 years ago by ★ 5.2k
0
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4
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1.7k
views
DiffBind
ATACSeq DiFFBind
3.8 years ago • updated 3.7 years ago Riba Michela ▴ 90
1
vote
5
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2.2k
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 3.9 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 4.0 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
3.2k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.3 years ago by ★ 5.2k • written 4.3 years ago by ▴ 70
0
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4
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2.4k
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
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12k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by • 0
0
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7
replies
2.1k
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
replies
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 5.9 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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4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by ▴ 10
0
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2
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1.4k
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
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Replies
Comment: Overcoming confounding in batch effect correction by Dario Strbenac ★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Comment: Overcoming confounding in batch effect correction by ATpoint ★ 4.7k
biostars.org and the [bioinformatics reddit][1] are suitable and have much larger audience than this forum here. [1]: https://www.reddi…
Comment: Overcoming confounding in batch effect correction by bbao ▴ 10
Thank you! And apologies for posting here. Do you know which forum I should go to in the future for questions like these?
Comment: For some reason I can't update BiocManager to 3.20 by shepherl 4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction by ATpoint ★ 4.7k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Votes
Answer: Store Matrix in DataFrame Cell
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
Comment: Overcoming confounding in batch effect correction
Overcoming confounding in batch effect correction
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