Showing : atacseq • reset
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 5 days ago by ★ 4.5k • written 6 days ago by • 0
0
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0
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76
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diffbind covariates
DiffBind ATACSeq
updated 11 days ago by 42k • written 12 days ago by ▴ 220
2
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5
replies
637
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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
7 weeks ago ronin • 0
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0
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349
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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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534
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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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314
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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
reply
557
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
9 months ago isaromero8888 • 0
0
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0
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554
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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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612
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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
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
replies
1.4k
views
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
0
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1
reply
821
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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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786
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
0
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0
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872
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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
reply
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
2.6 years ago • updated 2.5 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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769
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.7 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
0
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3
replies
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
votes
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
1
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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
votes
5
replies
4.3k
views
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
3.6 years ago • updated 3.5 years ago Riba Michela ▴ 90
1
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5
replies
2.1k
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
votes
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
vote
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
replies
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 4.3 years ago by • 0
0
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7
replies
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
votes
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
votes
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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Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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