Showing : ATACseq • reset
0
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2.3k
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DiffBind can't find a DAR
dar ATACSeq DiffBind
8 months ago • updated 7 months ago Mengjun • 0
0
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0
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346
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
8 months ago info ▴ 10
0
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1
reply
940
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
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0
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393
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diffbind covariates
DiffBind ATACSeq
updated 13 months ago by 43k • written 13 months ago by ▴ 220
2
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5
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1.2k
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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
14 months ago ronin • 0
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0
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1.0k
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
18 months ago Raghad • 0
0
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4
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968
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
19 months ago lonn • 0
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0
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617
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
20 months ago Pierre Lindenbaum ▴ 10
0
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1
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1.0k
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
22 months ago isaromero8888 • 0
0
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0
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944
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
22 months ago Jawahar • 0
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0
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679
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
23 months ago inna.gur • 0
0
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7
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1.7k
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ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 21 months ago by ▴ 10 • written 2.0 years ago by • 0
0
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0
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972
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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2
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2.0k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.4 years ago by ★ 1.6k • written 2.4 years ago by • 0
4
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6
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1.7k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.6 years ago Chris ▴ 20
5
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8
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1.9k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.7 years ago by ▴ 20
3
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5
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1.6k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.6 years ago by 68k • written 2.7 years ago by ▴ 20
8
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13
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5.5k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.7 years ago Chris ▴ 20
2
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1
reply
4.2k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 20
0
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1
reply
1.2k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.8 years ago by ★ 5.2k • written 2.8 years ago by • 0
0
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1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
0
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0
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1.1k
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
3.0 years ago gogniu • 0
0
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2
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2.1k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.3 years ago by • 0 • written 3.3 years ago by • 0
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
3.4 years ago Sebastian Lewandowski • 0
0
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1
reply
2.1k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.4 years ago by ★ 5.2k • written 3.5 years ago by • 0
2
votes
3
replies
1.6k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.6 years ago • updated 3.5 years ago bers.anthrope ▴ 10
1
vote
3
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2.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 2.0 years ago by • 0 • written 3.6 years ago by • 0
0
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0
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984
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.7 years ago hyjforesight • 0
2
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5
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6.9k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.3 years ago by ▴ 20 • written 4.2 years ago by ▴ 20
0
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3
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1.8k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.3 years ago by ★ 5.2k • written 4.2 years ago by ▴ 40
1
vote
3
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2.4k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.4 years ago by ▴ 80 • written 4.4 years ago by • 0
5
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8
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3.3k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.5 years ago by ▴ 20 • written 4.4 years ago by ▴ 30
1
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4
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2.3k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.5 years ago sh.kazempour94 ▴ 10
2
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5
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5.7k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.0 years ago by • 0 • written 4.5 years ago by ★ 5.2k
0
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4
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2.1k
views
DiffBind
ATACSeq DiFFBind
4.6 years ago Riba Michela ▴ 90
1
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5
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2.6k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
2
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4
replies
2.3k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.8 years ago by ★ 5.2k • written 4.8 years ago by • 0
1
vote
1
reply
2.2k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.1 years ago by ★ 5.2k
1
vote
10
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3.9k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.1 years ago by ★ 5.2k • written 5.1 years ago by ▴ 70
0
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4
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3.0k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.3 years ago by ★ 1.3k • written 5.3 years ago by • 0
1
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2
replies
14k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.3 years ago by ★ 1.3k • written 5.3 years ago by • 0
0
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7
replies
2.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.5 years ago by ★ 13k • written 6.5 years ago by • 0
0
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2
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1.8k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.6 years ago tangming2005 ▴ 200
2
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1
reply
2.0k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by ▴ 10
1
vote
2
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2.5k
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 6.8 years ago by 43k • written 6.8 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by ▴ 10
0
votes
2
replies
1.8k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 7.5 years ago by • 0 • written 7.5 years ago by ▴ 30
47 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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