Showing : ATACSeq • reset
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 6 weeks ago by ★ 4.6k • written 7 weeks ago by • 0
0
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0
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126
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diffbind covariates
DiffBind ATACSeq
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 220
2
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5
replies
704
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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
3 months ago ronin • 0
0
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0
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446
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
7 months ago Raghad • 0
0
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4
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563
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 months ago lonn • 0
0
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0
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346
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
8 months ago Pierre Lindenbaum ▴ 10
0
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1
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610
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
11 months ago isaromero8888 • 0
0
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0
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626
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
11 months ago Jawahar • 0
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0
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454
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
11 months ago inna.gur • 0
0
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7
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1.2k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 9 months ago by ▴ 10 • written 12 months ago by • 0
0
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0
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647
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 14 months ago by 67k • written 14 months ago by • 0
0
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2
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1.4k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 17 months ago by ★ 1.6k • written 17 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
20 months ago Chris ▴ 20
5
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8
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1.4k
views
Help with error install csaw
ChIPSeq ATACSeq
written 21 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 20 months ago by 67k • written 20 months ago by ▴ 20
8
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13
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4.1k
views
Help with Error in DiffBind
DiffBind ATACSeq
21 months ago • updated 20 months ago Chris ▴ 20
2
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1
reply
3.0k
views
DiffBind on ATAC seq data
ATACSeq
updated 21 months ago by ★ 5.2k • written 21 months ago by ▴ 20
0
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1
reply
863
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DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 22 months ago by ★ 5.2k • written 22 months ago by • 0
0
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1
reply
779
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
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0
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815
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.1 years ago gogniu • 0
0
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2
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1.7k
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long computing time for TSS enrichment score
ATACSeq
updated 16 months ago by • 0 • written 2.3 years ago by • 0
0
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0
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896
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.4 years ago Sebastian Lewandowski • 0
0
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1
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1.7k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
2
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3
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1.2k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.7 years ago • updated 2.6 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 12 months ago by • 0 • written 2.6 years ago by • 0
0
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0
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788
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.8 years ago hyjforesight • 0
2
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5
replies
5.6k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.4 years ago by ▴ 20 • written 3.2 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 2.3 years ago by ★ 5.2k • written 3.2 years ago by ▴ 40
1
vote
3
replies
1.9k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.4 years ago by ▴ 80 • written 3.4 years ago by • 0
5
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8
replies
2.7k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.5 years ago by ▴ 20 • written 3.4 years ago by ▴ 30
1
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4
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1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.5 years ago sh.kazempour94 ▴ 10
2
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5
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4.5k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.0 years ago by • 0 • written 3.6 years ago by ★ 5.2k
0
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4
replies
1.7k
views
DiffBind
ATACSeq DiFFBind
3.7 years ago • updated 3.6 years ago Riba Michela ▴ 90
1
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5
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2.1k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.7 years ago by 67k • written 3.8 years ago by • 0
2
votes
4
replies
1.9k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.8 years ago by ★ 5.2k • written 3.8 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 4.1 years ago by ★ 5.2k
1
vote
10
replies
3.0k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.1 years ago by ★ 5.2k • written 4.2 years ago by ▴ 70
0
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4
replies
2.3k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by • 0
1
vote
2
replies
11k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.3 years ago by ★ 1.3k • written 4.4 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 5.5 years ago by ★ 13k • written 5.5 years ago by • 0
0
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2
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1.4k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.6 years ago tangming2005 ▴ 200
2
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1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.7 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
1
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2
replies
2.2k
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 5.8 years ago by 43k • written 5.8 years ago by • 0
2
votes
4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.2 years ago by ★ 5.2k • written 6.3 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 6.5 years ago by • 0 • written 6.5 years ago by ▴ 30
45 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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