Showing : ATACSeq • reset
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ATACseq rudimentary questions
ATACSeq DiffBind
5 weeks ago • updated 4 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 • updated 9 months ago Mengjun • 0
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0
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414
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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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0
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472
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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
16 months ago ronin • 0
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1.2k
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
20 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 • updated 21 months ago lonn • 0
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704
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
22 months ago Pierre Lindenbaum ▴ 10
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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
2.0 years ago isaromero8888 • 0
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1.0k
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
2.0 years ago Jawahar • 0
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735
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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
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1.0k
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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2
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2.2k
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
4
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6
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1.8k
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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
views
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 2.8 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 • updated 2.8 years ago Chris ▴ 20
2
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1
reply
4.6k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.9 years ago by ★ 5.3k • written 2.9 years ago by ▴ 20
0
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1
reply
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
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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
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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2.1k
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long computing time for TSS enrichment score
ATACSeq
updated 2.5 years ago by • 0 • written 3.4 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
3.5 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 3.6 years ago by • 0
2
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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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1.0k
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[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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7.2k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.5 years ago by ▴ 20 • written 4.3 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 4.3 years ago by ▴ 40
1
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3
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2.5k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.5 years ago by ▴ 80 • written 4.6 years ago by • 0
5
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8
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3.4k
views
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
4.6 years ago sh.kazempour94 ▴ 10
2
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5
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5.9k
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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
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2.4k
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DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.9 years ago by ★ 5.3k • written 5.0 years ago by • 0
1
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1
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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 5.2 years ago by ★ 5.3k • written 5.3 years ago by ▴ 70
0
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4
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3.2k
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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2.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.6 years ago by ★ 13k • written 6.6 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
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4
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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 7.6 years ago by • 0 • written 7.7 years ago by ▴ 30
48 results • Page 1 of 1
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Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
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Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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