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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180
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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
778
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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
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546
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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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608
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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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385
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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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687
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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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689
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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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489
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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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699
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 16 months ago by 68k • written 16 months ago by • 0
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2
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1.5k
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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
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Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
3
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5
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1.2k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 21 months ago by 68k • 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
3.3k
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
903
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 24 months ago by ★ 5.2k • written 2.0 years ago by • 0
0
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1
reply
801
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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863
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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930
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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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807
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
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1.4k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.5 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 3.6 years ago by • 0
5
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8
replies
2.8k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.7 years ago by ▴ 20 • written 3.6 years ago by ▴ 30
1
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4
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1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.7 years ago • updated 3.6 years ago sh.kazempour94 ▴ 10
2
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5
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4.7k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.2 years ago by • 0 • written 3.7 years ago by ★ 5.2k
0
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4
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1.7k
views
DiffBind
ATACSeq DiFFBind
3.8 years ago • updated 3.7 years ago Riba Michela ▴ 90
1
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5
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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 68k • 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 4.0 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
3.2k
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
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2.4k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by • 0
1
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2
replies
12k
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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
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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
5.8 years ago tangming2005 ▴ 200
2
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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
votes
4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.4 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 6.7 years ago by ▴ 30
45 results • Page 1 of 1
Recent ...
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Answer: DESeq2 adujsted p-value cutoff seemingly not working by James W. MacDonald 68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by SofieK • 0
Thank you, I will try this and see.
Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexploitss • 0
Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…
Comment: GenomeInfoDbData cannot install in R and warning had non-zero exit status by Renuka • 0
how you did it pls explain
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = by James W. MacDonald 68k
If I understand correctly, you want to assess differential transcript abundances. If so, there are a couple of ways you can do that. One wa…
Votes
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
Comment: Unused arguments error without used arguments in GSVA?
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