Showing : ATACseq • reset
8
votes
13
replies
5.9k
views
Help with Error in DiffBind
DiffBind ATACSeq
3.0 years ago • updated 2.9 years ago Chris ▴ 20
1
vote
10
replies
4.4k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.3 years ago by ★ 5.3k • written 5.4 years ago by ▴ 70
5
votes
8
replies
2.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 3.0 years ago by ▴ 20
5
votes
8
replies
3.5k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.8 years ago by ▴ 20 • written 4.7 years ago by ▴ 30
0
votes
7
replies
1.9k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 2.0 years ago by ▴ 10 • written 2.3 years ago by • 0
0
votes
7
replies
2.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.7 years ago by ★ 13k • written 6.7 years ago by • 0
4
votes
6
replies
1.9k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.9 years ago Chris ▴ 20
1
vote
5
replies
2.7k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
2
votes
5
replies
1.4k
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
18 months ago ronin • 0
3
votes
5
replies
1.7k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 20
2
votes
5
replies
7.4k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.6 years ago by ▴ 20 • written 4.4 years ago by ▴ 20
2
votes
5
replies
6.1k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.3 years ago by • 0 • written 4.8 years ago by ★ 5.3k
0
votes
4
replies
2.5k
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
11 months ago Mengjun • 0
2
votes
4
replies
2.1k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 7.5 years ago by ★ 5.3k • written 7.5 years ago by ▴ 10
0
votes
4
replies
2.3k
views
DiffBind
ATACSeq DiFFBind
4.9 years ago • updated 4.8 years ago Riba Michela ▴ 90
0
votes
4
replies
3.5k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by • 0
1
vote
4
replies
2.5k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.7 years ago sh.kazempour94 ▴ 10
2
votes
4
replies
2.4k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 5.0 years ago by ★ 5.3k • written 5.0 years ago by • 0
0
votes
4
replies
1.0k
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
23 months ago lonn • 0
1
vote
3
replies
2.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 2.3 years ago by • 0 • written 3.9 years ago by • 0
1
vote
3
replies
2.6k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.6 years ago by ▴ 80 • written 4.6 years ago by • 0
0
votes
3
replies
1.9k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.6 years ago by ★ 5.3k • written 4.4 years ago by ▴ 40
2
votes
3
replies
1.8k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.9 years ago • updated 3.8 years ago bers.anthrope ▴ 10
1
vote
2
replies
2.4k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.6 years ago by ★ 1.6k • written 2.6 years ago by ▴ 10
1
vote
2
replies
2.7k
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 7.0 years ago by 43k • written 7.0 years ago by • 0
0
votes
2
replies
1.9k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.9 years ago tangming2005 ▴ 200
1
vote
2
replies
15k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.6 years ago by ★ 1.4k • written 5.6 years ago by • 0
0
votes
2
replies
2.1k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 7.7 years ago by • 0 • written 7.8 years ago by ▴ 30
0
votes
2
replies
2.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.6 years ago by • 0 • written 3.5 years ago by • 0
0
votes
2
replies
273
views
ATACseq rudimentary questions
ATACSeq DiffBind
10 weeks ago 4747 • 0
0
votes
1
reply
1.2k
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
0
votes
1
reply
1.4k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 3.1 years ago by ★ 5.3k • written 3.1 years ago by • 0
0
votes
1
reply
1.2k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
2.1 years ago isaromero8888 • 0
2
votes
1
reply
4.9k
views
DiffBind on ATAC seq data
ATACSeq
updated 3.0 years ago by ★ 5.3k • written 3.0 years ago by ▴ 20
2
votes
1
reply
2.1k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 7.0 years ago by ★ 5.3k • written 7.0 years ago by ▴ 10
1
vote
1
reply
2.4k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.4 years ago by ★ 5.3k
0
votes
1
reply
1.2k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
0
votes
1
reply
2.4k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.7 years ago by ★ 5.3k • written 3.7 years ago by • 0
0
votes
0
replies
449
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
11 months ago info ▴ 10
0
votes
0
replies
742
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
23 months ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
1.1k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
2.1 years ago Jawahar • 0
0
votes
0
replies
1.0k
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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0
replies
1.2k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
22 months ago Raghad • 0
0
votes
0
replies
1.2k
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
3.3 years ago gogniu • 0
0
votes
0
replies
1.2k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.6 years ago Sebastian Lewandowski • 0
0
votes
0
replies
520
views
diffbind covariates
DiffBind ATACSeq
updated 16 months ago by 43k • written 16 months ago by ▴ 220
0
votes
0
replies
764
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
2.2 years ago inna.gur • 0
0
votes
0
replies
1.1k
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
4.0 years ago hyjforesight • 0
48 results • Page 1 of 1
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Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…
Votes
DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
A: Removing cell cycle genes in large data set integration
A: Removing cell cycle genes in large data set integration
Answer: Quick two questions on limpa
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