Showing : ATACSeq • reset
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
18 days ago Pierre Lindenbaum ▴ 10
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272
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
11 weeks ago isaromero8888 • 0
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214
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 weeks ago Jawahar • 0
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227
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
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7
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611
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 6 weeks ago by ▴ 10 • written 4 months ago by • 0
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374
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
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2
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777
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 8 months ago by ★ 1.6k • written 8 months ago by • 0
4
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6
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884
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Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
12 months ago Chris • 0
3
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5
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820
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How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by 65k • written 12 months ago by • 0
5
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8
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983
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Help with error install csaw
ChIPSeq ATACSeq
written 12 months ago by • 0
8
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13
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2.7k
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Help with Error in DiffBind
DiffBind ATACSeq
12 months ago Chris • 0
2
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1
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1.5k
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DiffBind on ATAC seq data
ATACSeq
updated 12 months ago by ★ 5.1k • written 12 months ago by • 0
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1
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640
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 14 months ago by ★ 5.1k • written 14 months ago by • 0
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1
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536
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Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
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542
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
17 months ago gogniu • 0
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2
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1.2k
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long computing time for TSS enrichment score
ATACSeq
updated 7 months ago by • 0 • written 19 months ago by • 0
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698
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
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1
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1.3k
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Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 21 months ago by ★ 5.1k • written 22 months ago by • 0
1
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3
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1.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 4 months ago by • 0 • written 23 months ago by • 0
2
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3
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928
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
24 months ago • updated 23 months ago bers.anthrope • 0
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557
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[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.1 years ago hyjforesight • 0
2
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5
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4.3k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 20 months ago by ▴ 20 • written 2.5 years ago by ▴ 20
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3
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1.1k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 20 months ago by ★ 5.1k • written 2.5 years ago by ▴ 30
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3
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1.4k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 2.7 years ago by ▴ 80 • written 2.7 years ago by • 0
5
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8
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2.1k
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 22 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
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4
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1.5k
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Binding matrix created by DiffBind
ATACSeq DiffBind
2.8 years ago sh.kazempour94 ▴ 10
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5
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3.2k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 16 months ago by • 0 • written 2.9 years ago by ★ 5.1k
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4
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1.3k
views
DiffBind
ATACSeq DiFFBind
3.0 years ago • updated 2.9 years ago Riba Michela ▴ 90
1
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5
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1.7k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.1 years ago by 65k • written 3.1 years ago by • 0
2
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4
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1.5k
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DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.1 years ago by ★ 5.1k • written 3.1 years ago by • 0
1
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1
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1.5k
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News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 3.5 years ago by ★ 5.1k
1
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10
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2.2k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 3.4 years ago by ★ 5.1k • written 3.5 years ago by ▴ 70
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4
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1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 3.6 years ago by ★ 1.3k • written 3.7 years ago by • 0
1
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2
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9.1k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
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7
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1.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.8 years ago by ★ 13k • written 4.8 years ago by • 0
0
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2
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1.2k
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calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
4.9 years ago tangming2005 ▴ 190
2
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1
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1.3k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.1 years ago by ★ 5.1k • written 5.1 years ago by ▴ 10
1
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2
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2.0k
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 5.1 years ago by 41k • written 5.1 years ago by • 0
2
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4
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1.4k
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DiffBind confuses coordinates of peaks
atacseq diffbind
updated 5.5 years ago by ★ 5.1k • written 5.6 years ago by ▴ 10
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2
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1.1k
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mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 5.8 years ago by • 0 • written 5.8 years ago by ▴ 30
40 results • Page 1 of 1
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Comment: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var by daniel.carbajo • 0
Yeah I think this is the way to go! How can I pass `col_list` here though? `Heatmap` does not accept a list of color vectors... How can I m…
Answer: The issue with SGSeq_analyzeFeatures() returns errors on BAM files by kamryncole1963 • 0
https://support.bioconductor.org/p/85837/[tunnel rush][1] Refer to this link, it may help. [1]: https://tunnelrush3.com
Comment: flowStats Search Error by SamGG ▴ 350
So do I. The direct URL is https://bioconductor.org/packages/3.18/bioc/html/flowStats.html
Comment: Interaction Terms in DESeq2 - Shrinkage by andrebolerbarros ▴ 20
Thanks for your suggestion! For `apeglm` shrinkage, on that scenario, I would have to relevel the variable and then re-run with `nbinomWal…
Answer: Interaction Terms in DESeq2 - Shrinkage by swbarnes2 ★ 1.3k
I think the simpler way to do it is to make a new column of conc_time_tissue all stuck together, and make that column your design. Then …
Votes
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
Answer: How to retrieve detailed regression results from deseq2
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