Showing : diffbind • reset
1
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7.3k
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DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.7 years ago by ▴ 10
0
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0
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262
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DiffBind plot.profile error
BiocParallel DiffBind
6 months ago this_is_me_trying • 0
0
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0
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1.1k
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Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq profileplyr DiffBind
7 months ago Muhammad • 0
0
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0
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360
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I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
8 months ago atlanta • 0
0
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4
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2.3k
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DiffBind can't find a DAR
dar ATACSeq DiffBind
8 months ago Mengjun • 0
0
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0
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262
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DiffBind multi-tissue comparison
DiffBind
9 months ago lryrainche • 0
1
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8
replies
2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
9 months ago • updated 8 months ago Luca • 0
0
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0
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376
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DiffBind recommendation on using IgG bams
peakcalling DiffBind
9 months ago Harish • 0
0
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4
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1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR DiffBind
updated 9 months ago by • 0 • written 9 months ago by • 0
0
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1
reply
463
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building samplesheet and plot profile
DiffBind
10 months ago yf • 0
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5
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855
views
Diffbind interpretation of data - fold change
DiffBind
11 months ago Vera • 0
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0
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609
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
13 months ago kim • 0
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0
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409
views
diffbind covariates
DiffBind ATACSeq
updated 13 months ago by 43k • written 13 months ago by ▴ 220
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2
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984
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DiffBind dba.report discrepancy
DiffBind
14 months ago • updated 13 months ago aelbassiouny • 0
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0
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359
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DiffBind subset replicates
DiffBind
14 months ago Haiping • 0
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0
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640
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Background normalization of Diffbind dba.normalize
Normalization DiffBind
14 months ago Young Boqin • 0
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0
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519
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
15 months ago Alejandro • 0
0
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2
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646
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DiffBind for MBD-seq
MBD-seq DiffBind
15 months ago Marianna ▴ 20
0
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1
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742
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DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
16 months ago • updated 10 months ago Ian D. ▴ 70
0
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1
reply
630
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
16 months ago mdidish ▴ 10
0
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0
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536
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DiffBind dba.plotprofile y-axis range
DiffBind
16 months ago Tara • 0
0
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8
replies
1.4k
views
DiffBind full library size not reliable
DiffBind Reads MACS2 FullLibSize
updated 16 months ago by ★ 5.2k • written 16 months ago by ▴ 20
1
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3
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939
views
Create merged ChIP heatmap across conditions
DiffBind profileplyr
updated 17 months ago by ★ 5.2k • written 17 months ago by • 0
0
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0
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820
views
Blacklist regions on DBA object (diffbind)
DiffBind chipseq
17 months ago gamma.jian ▴ 10
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2
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988
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind DifferentialPeakCalling
18 months ago Mallory • 0
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0
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530
views
Difference in Contrast in DiffBind
DiffBind
19 months ago user_bioinfo • 0
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0
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529
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
19 months ago Dinesh • 0
0
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1
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1.1k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 13 months ago by • 0 • written 19 months ago by ▴ 10
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0
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833
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
19 months ago yvonneh • 0
0
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0
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477
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 months ago Ian D. ▴ 70
0
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9
replies
2.0k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
19 months ago • updated 14 months ago Ian D. ▴ 70
3
votes
1
reply
902
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 19 months ago by 43k • written 19 months ago by ▴ 10
0
votes
1
reply
1.3k
views
ATACseq merge peaks
DiffBind
updated 19 months ago by ★ 5.0k • written 20 months ago by • 0
0
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4
replies
975
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
20 months ago lonn • 0
0
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0
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546
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
20 months ago Virangika • 0
2
votes
2
replies
1.1k
views
[DiffBind] Obtaining normalization factors
DiffBind
20 months ago Henry ▴ 10
2
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2
replies
1.8k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
20 months ago Henry ▴ 10
0
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0
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655
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
20 months ago feather-W • 0
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0
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643
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
20 months ago Ankit ▴ 20
0
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0
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626
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
20 months ago Pierre Lindenbaum ▴ 10
0
votes
0
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589
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
21 months ago erbrocato • 0
0
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2
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943
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
21 months ago Sam ▴ 10
0
votes
1
reply
791
views
Exact same results in Diffbind with different normalization methods
DiffBind
21 months ago red_bricks ▴ 60
0
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1
reply
1.0k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
23 months ago isaromero8888 • 0
0
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0
replies
949
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
23 months ago Jawahar • 0
0
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0
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612
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
23 months ago frueher • 0
0
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0
replies
564
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
23 months ago Aswathy • 0
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0
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804
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
23 months ago Hai • 0
0
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0
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686
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
23 months ago inna.gur • 0
2
votes
2
replies
2.0k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 7 months ago by • 0 • written 2.3 years ago by ▴ 10
678 results • Page 1 of 14
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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
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