Showing : ATACSeq • reset
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 2 days ago by ★ 4.5k • written 4 days ago by • 0
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0
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63
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diffbind covariates
DiffBind ATACSeq
updated 9 days ago by 42k • written 10 days ago by ▴ 220
2
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5
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636
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
7 weeks ago • updated 6 weeks ago ronin • 0
0
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0
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344
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
5 months ago Raghad • 0
0
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4
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528
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 months ago lonn • 0
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0
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312
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 months ago Pierre Lindenbaum ▴ 10
0
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1
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551
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
9 months ago isaromero8888 • 0
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0
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551
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
9 months ago Jawahar • 0
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0
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429
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
10 months ago inna.gur • 0
0
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7
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1.1k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 8 months ago by ▴ 10 • written 11 months ago by • 0
0
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0
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610
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 13 months ago by 67k • written 13 months ago by • 0
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2
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1.3k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 15 months ago by ★ 1.6k • written 15 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
18 months ago Chris ▴ 20
5
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8
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1.4k
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Help with error install csaw
ChIPSeq ATACSeq
written 19 months ago by ▴ 20
3
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5
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1.1k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 18 months ago by 67k • written 19 months ago by ▴ 20
8
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13
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3.8k
views
Help with Error in DiffBind
DiffBind ATACSeq
19 months ago Chris ▴ 20
2
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1
reply
2.7k
views
DiffBind on ATAC seq data
ATACSeq
updated 19 months ago by ★ 5.2k • written 19 months ago by ▴ 20
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1
reply
819
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 21 months ago by ★ 5.2k • written 21 months ago by • 0
0
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1
reply
756
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 22 months ago by ★ 1.3k • written 22 months ago by • 0
0
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0
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783
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
23 months ago gogniu • 0
0
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2
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1.6k
views
long computing time for TSS enrichment score
ATACSeq
updated 14 months ago by • 0 • written 2.2 years ago by • 0
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0
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871
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.3 years ago Sebastian Lewandowski • 0
0
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1
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1.7k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.4 years ago by • 0
2
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3
replies
1.2k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.5 years ago • updated 2.4 years ago bers.anthrope ▴ 10
1
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3
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1.9k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 11 months ago by • 0 • written 2.5 years ago by • 0
0
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0
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764
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.6 years ago hyjforesight • 0
2
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5
replies
5.4k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.2 years ago by ▴ 20 • written 3.1 years ago by ▴ 20
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3
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1.3k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.2 years ago by ★ 5.2k • written 3.1 years ago by ▴ 40
1
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3
replies
1.9k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.3 years ago by ▴ 80 • written 3.3 years ago by • 0
5
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8
replies
2.6k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.4 years ago by ▴ 20 • written 3.3 years ago by ▴ 30
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4
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1.8k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.4 years ago sh.kazempour94 ▴ 10
2
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5
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4.2k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 23 months ago by • 0 • written 3.5 years ago by ★ 5.2k
0
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4
replies
1.6k
views
DiffBind
ATACSeq DiFFBind
3.5 years ago Riba Michela ▴ 90
1
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5
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2.0k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
2
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4
replies
1.9k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
1
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1
reply
1.8k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.0 years ago by ★ 5.2k
1
vote
10
replies
2.9k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.0 years ago by ★ 5.2k • written 4.0 years ago by ▴ 70
0
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4
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2.2k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.2 years ago by ★ 1.3k • written 4.2 years ago by • 0
1
vote
2
replies
11k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.2 years ago by ★ 1.3k • written 4.2 years ago by • 0
0
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7
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2.0k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.4 years ago by ★ 13k • written 5.4 years ago by • 0
0
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2
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1.4k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.5 years ago tangming2005 ▴ 200
2
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1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
1
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2
replies
2.2k
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 5.7 years ago by 42k • written 5.7 years ago by • 0
2
votes
4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
0
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2
replies
1.3k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.4 years ago by • 0 • written 6.4 years ago by ▴ 30
45 results • Page 1 of 1
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Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim by Ai • 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2 by icecreamlover • 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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