Showing : atacseq • reset
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ATACseq rudimentary questions
ATACSeq DiffBind
6 weeks ago 4747 • 0
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4
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2.5k
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DiffBind can't find a DAR
dar ATACSeq DiffBind
10 months ago Mengjun • 0
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423
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
10 months ago info ▴ 10
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1
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1.1k
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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484
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diffbind covariates
DiffBind ATACSeq
updated 15 months ago by 43k • written 15 months ago by ▴ 220
2
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5
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1.3k
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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
17 months ago ronin • 0
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1.2k
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
21 months ago Raghad • 0
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4
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1.0k
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
22 months ago lonn • 0
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713
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
22 months ago Pierre Lindenbaum ▴ 10
0
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1
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1.2k
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
2.1 years ago isaromero8888 • 0
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1.1k
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
2.1 years ago Jawahar • 0
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744
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
2.1 years ago inna.gur • 0
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7
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1.9k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 23 months ago by ▴ 10 • written 2.2 years ago by • 0
0
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0
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1.0k
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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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2
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2.3k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.6 years ago by ★ 1.6k • written 2.6 years ago by • 0
4
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6
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1.8k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.8 years ago Chris ▴ 20
5
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8
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2.0k
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Help with error install csaw
ChIPSeq ATACSeq
written 2.9 years ago by ▴ 20
3
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5
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1.7k
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How to annotate genes from results of DiffBind
ATACSeq
updated 2.8 years ago by 68k • written 2.9 years ago by ▴ 20
8
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13
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5.7k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.9 years ago Chris ▴ 20
2
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1
reply
4.6k
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DiffBind on ATAC seq data
ATACSeq
updated 2.9 years ago by ★ 5.3k • written 2.9 years ago by ▴ 20
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1
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1.3k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 3.0 years ago by ★ 5.3k • written 3.0 years ago by • 0
0
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1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 3.1 years ago by ★ 1.3k • written 3.1 years ago by • 0
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0
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1.2k
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How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
3.2 years ago gogniu • 0
0
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2
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2.2k
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long computing time for TSS enrichment score
ATACSeq
updated 2.5 years ago by • 0 • written 3.5 years ago by • 0
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0
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1.2k
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.6 years ago Sebastian Lewandowski • 0
0
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1
reply
2.2k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.6 years ago by ★ 5.3k • written 3.7 years ago by • 0
2
votes
3
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1.7k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.8 years ago • updated 3.7 years ago bers.anthrope ▴ 10
1
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3
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2.6k
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regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 2.2 years ago by • 0 • written 3.8 years ago by • 0
0
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0
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1.1k
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.9 years ago hyjforesight • 0
2
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5
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7.3k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.5 years ago by ▴ 20 • written 4.4 years ago by ▴ 20
0
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3
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1.9k
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package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.5 years ago by ★ 5.3k • written 4.4 years ago by ▴ 40
1
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3
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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
5
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8
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3.5k
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.7 years ago by ▴ 20 • written 4.6 years ago by ▴ 30
1
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4
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2.4k
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Binding matrix created by DiffBind
ATACSeq DiffBind
4.7 years ago • updated 4.6 years ago sh.kazempour94 ▴ 10
2
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5
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5.9k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.2 years ago by • 0 • written 4.7 years ago by ★ 5.3k
0
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4
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2.2k
views
DiffBind
ATACSeq DiFFBind
4.8 years ago • updated 4.7 years ago Riba Michela ▴ 90
1
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5
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2.7k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
2
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4
replies
2.4k
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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
1
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1
reply
2.4k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.3 years ago by ★ 5.3k
1
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10
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4.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.3 years ago by ★ 5.3k • written 5.3 years ago by ▴ 70
0
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4
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3.3k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by • 0
1
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2
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15k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.5 years ago by ★ 1.3k • written 5.5 years ago by • 0
0
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7
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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
0
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2
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1.9k
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calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.8 years ago tangming2005 ▴ 200
2
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1
reply
2.1k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.9 years ago by ★ 5.3k • written 6.9 years ago by ▴ 10
1
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2
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2.6k
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 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
4
replies
2.1k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 7.4 years ago by ★ 5.3k • written 7.4 years ago by ▴ 10
0
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2
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2.0k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 7.7 years ago by • 0 • written 7.7 years ago by ▴ 30
48 results • Page 1 of 1
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
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Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
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