Showing : ATACseq • reset
8
votes
13
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4.2k
views
Help with Error in DiffBind
DiffBind ATACSeq
22 months ago • updated 21 months ago Chris ▴ 20
5
votes
8
replies
2.7k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.6 years ago by ▴ 20 • written 3.5 years ago by ▴ 30
5
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8
replies
1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
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
3
votes
5
replies
1.2k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 21 months ago by 67k • written 21 months ago by ▴ 20
2
votes
4
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1.9k
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 3.9 years ago by • 0
2
votes
5
replies
5.7k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.4 years ago by ▴ 20 • written 3.3 years ago by ▴ 20
2
votes
1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
2
votes
1
reply
3.1k
views
DiffBind on ATAC seq data
ATACSeq
updated 22 months ago by ★ 5.2k • written 22 months ago by ▴ 20
2
votes
5
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4.6k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.1 years ago by • 0 • written 3.6 years ago by ★ 5.2k
2
votes
3
replies
1.2k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.7 years ago • updated 2.6 years ago bers.anthrope ▴ 10
2
votes
5
replies
735
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
4 months ago • updated 3 months ago ronin • 0
2
votes
4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
1
vote
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
1
vote
3
replies
2.0k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 13 months ago by • 0 • written 2.7 years ago by • 0
1
vote
5
replies
2.2k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
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 3.5 years ago by • 0
1
vote
1
reply
1.9k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.2 years ago by ★ 5.2k
1
vote
2
replies
11k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
1
vote
4
replies
1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.6 years ago sh.kazempour94 ▴ 10
1
vote
10
replies
3.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by ▴ 70
0
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0
replies
153
views
diffbind covariates
DiffBind ATACSeq
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 220
0
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0
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470
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
12 months ago inna.gur • 0
0
votes
2
replies
1.4k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 30
0
votes
1
reply
393
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
0
votes
2
replies
1.4k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.7 years ago tangming2005 ▴ 200
0
votes
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
votes
4
replies
2.3k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
0
votes
4
replies
584
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 months ago lonn • 0
0
votes
1
reply
885
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 23 months ago by ★ 5.2k • written 23 months ago by • 0
0
votes
4
replies
1.7k
views
DiffBind
ATACSeq DiFFBind
3.7 years ago Riba Michela ▴ 90
0
votes
7
replies
1.2k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 10 months ago by ▴ 10 • written 13 months ago by • 0
0
votes
0
replies
909
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.5 years ago Sebastian Lewandowski • 0
0
votes
0
replies
497
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
7 months ago Raghad • 0
0
votes
1
reply
794
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
0
votes
0
replies
661
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
11 months ago Jawahar • 0
0
votes
1
reply
1.8k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
votes
2
replies
1.5k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 17 months ago by ★ 1.6k • written 18 months ago by • 0
0
votes
0
replies
673
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 15 months ago by 67k • written 15 months ago by • 0
0
votes
0
replies
846
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
votes
3
replies
1.4k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.4 years ago by ★ 5.2k • written 3.3 years ago by ▴ 40
0
votes
1
reply
646
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
11 months ago isaromero8888 • 0
0
votes
0
replies
795
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.8 years ago hyjforesight • 0
0
votes
2
replies
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
votes
0
replies
362
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
9 months ago Pierre Lindenbaum ▴ 10
45 results • Page 1 of 1
Recent ...
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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
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Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
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