Showing : ATACSeq • reset
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 3 months ago by ★ 4.6k • written 3 months ago by • 0
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0
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173
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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
replies
771
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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
0
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0
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535
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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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601
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 months ago lonn • 0
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0
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380
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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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677
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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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685
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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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485
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
13 months ago inna.gur • 0
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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696
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 16 months ago by 67k • written 16 months ago by • 0
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2
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1.5k
views
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
21 months ago Chris ▴ 20
5
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8
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1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
3
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5
replies
1.2k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 21 months ago by 67k • written 22 months ago by ▴ 20
8
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13
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4.3k
views
Help with Error in DiffBind
DiffBind ATACSeq
22 months ago Chris ▴ 20
2
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1
reply
3.2k
views
DiffBind on ATAC seq data
ATACSeq
updated 22 months ago by ★ 5.2k • written 22 months ago by ▴ 20
0
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1
reply
899
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 23 months ago by ★ 5.2k • written 2.0 years ago by • 0
0
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1
reply
798
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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860
views
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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1.7k
views
long computing time for TSS enrichment score
ATACSeq
updated 17 months ago by • 0 • written 2.4 years ago by • 0
0
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0
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924
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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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 2.6 years ago by • 0
2
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3
replies
1.2k
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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801
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
5.8k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.5 years ago by ▴ 20 • written 3.3 years ago by ▴ 20
0
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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
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
5
votes
8
replies
2.8k
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
1
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4
replies
1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.6 years ago sh.kazempour94 ▴ 10
2
votes
5
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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 3.7 years ago by ★ 5.2k
0
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4
replies
1.7k
views
DiffBind
ATACSeq DiFFBind
3.8 years ago • updated 3.7 years ago Riba Michela ▴ 90
1
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5
replies
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 67k • 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 3.9 years ago by ★ 5.2k • written 3.9 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
3.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.2 years ago by ★ 5.2k • written 4.3 years ago by ▴ 70
0
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4
replies
2.4k
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
1
vote
2
replies
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
votes
7
replies
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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2
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1.5k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.7 years ago tangming2005 ▴ 200
2
votes
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 6.3 years ago by ★ 5.2k • written 6.4 years ago by ▴ 10
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
45 results • Page 1 of 1
Recent ...
Replies
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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