Showing : ATACSeq • reset
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
3 days ago jfmay • 0
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0
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159
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 8 weeks ago by 64k • written 8 weeks ago by • 0
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2
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477
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 4 months ago by ★ 1.6k • written 4 months ago by • 0
4
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6
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675
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Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
7 months ago Chris • 0
5
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8
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723
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Help with error install csaw
ChIPSeq ATACSeq
updated 8 months ago by • 0 • written 8 months ago by • 0
3
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5
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653
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How to annotate genes from results of DiffBind
ATACSeq
updated 7 months ago by 64k • written 8 months ago by • 0
8
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13
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1.8k
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Help with Error in DiffBind
DiffBind ATACSeq
8 months ago Chris • 0
1
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1
reply
697
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DiffBind on ATAC seq data
ATACSeq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
0
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1
reply
436
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 9 months ago by ★ 5.1k • written 10 months ago by • 0
0
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1
reply
406
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 10 months ago by ★ 1.3k • written 10 months ago by • 0
0
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0
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377
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
12 months ago gogniu • 0
0
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2
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789
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long computing time for TSS enrichment score
ATACSeq
updated 3 months ago by • 0 • written 15 months ago by • 0
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0
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549
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
16 months ago Sebastian Lewandowski • 0
0
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1
reply
1.0k
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Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 17 months ago by ★ 5.1k • written 17 months ago by • 0
2
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3
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790
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DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
19 months ago • updated 18 months ago bers.anthrope • 0
1
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2
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1.2k
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regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
19 months ago zgraytho88 • 0
0
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0
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446
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
20 months ago hyjforesight • 0
2
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5
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3.7k
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using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 15 months ago by ▴ 20 • written 2.2 years ago by ▴ 20
0
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3
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937
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package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 15 months ago by ★ 5.1k • written 2.2 years ago by ▴ 30
1
vote
3
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1.2k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 2.4 years ago by ▴ 80 • written 2.4 years ago by • 0
5
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8
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1.9k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 18 months ago by ▴ 20 • written 2.4 years ago by ▴ 30
1
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4
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1.3k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
2.5 years ago • updated 2.4 years ago sh.kazempour94 ▴ 10
2
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5
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2.7k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 11 months ago by • 0 • written 2.5 years ago by ★ 5.1k
0
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4
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1.1k
views
DiffBind
ATACSeq DiFFBind
2.6 years ago • updated 2.5 years ago Riba Michela ▴ 90
1
vote
5
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1.5k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 2.7 years ago by 64k • written 2.7 years ago by • 0
2
votes
4
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1.3k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 2.8 years ago by ★ 5.1k • written 2.8 years ago by • 0
1
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1
reply
1.4k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.1 years ago by ★ 5.1k
1
vote
10
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1.8k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.1 years ago by ★ 5.1k • written 3.1 years ago by ▴ 70
0
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4
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1.7k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.3 years ago by ★ 1.3k • written 3.3 years ago by • 0
1
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2
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7.9k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.3 years ago by ★ 1.3k • written 3.3 years ago by • 0
0
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7
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1.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
0
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2
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1.0k
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calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
4.6 years ago tangming2005 ▴ 190
2
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1
reply
1.1k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 4.7 years ago by ★ 5.1k • written 4.7 years ago by ▴ 10
1
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2
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1.9k
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 4.7 years ago by 41k • written 4.7 years ago by • 0
2
votes
4
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1.3k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.2 years ago by ★ 5.1k • written 5.2 years ago by ▴ 10
0
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2
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1.0k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 5.5 years ago by • 0 • written 5.5 years ago by ▴ 30
36 results • Page 1 of 1
Recent ...
Replies
Comment: NCBI protein conversion to CDNA and NCBI gene (in R) by Gordon Smyth 48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by R_Page • 0
Thank you, this works well. As for CDNA, I figured out what I need to find, and have made a new post regarding it.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hello Michael, I am continuing here and need your expert answer on this again I have performed small rna loci and DNA methylation mappin…
Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Votes
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Why is DMRcate not available for Bioconductor version 3.18?
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