Showing : DiFFBind • reset
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56
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 14 hours ago by ★ 5.2k • written 1 day ago by ▴ 70
1
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1
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76
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
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1
reply
110
views
ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 7 days ago by • 0
0
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4
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226
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
14 days ago • updated 12 days ago lonn • 0
0
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0
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91
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
16 days ago Virangika • 0
2
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2
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166
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[DiffBind] Obtaining normalization factors
DiffBind
19 days ago • updated 16 days ago Henry ▴ 10
2
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2
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379
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
20 days ago • updated 19 days ago Henry ▴ 10
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0
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108
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
4 weeks ago feather-W • 0
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0
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108
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
4 weeks ago Ankit ▴ 20
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0
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93
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
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0
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138
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
0
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2
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241
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
0
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1
reply
194
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Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago red_bricks ▴ 50
0
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1
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297
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
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0
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244
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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0
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174
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
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0
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166
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
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0
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237
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
4 months ago Hai • 0
0
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0
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256
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
0
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1
reply
930
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
0
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2
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347
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
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2
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326
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
1
reply
353
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
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0
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330
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
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0
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404
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
2
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4
replies
1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 6 months ago by • 0 • written 7 months ago by • 0
2
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2
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462
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 6 months ago r.murakami • 0
1
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1
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447
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 7 months ago by 65k • written 7 months ago by • 0
3
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7
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857
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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3
replies
631
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by • 0 • written 7 months ago by • 0
0
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1
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543
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago Mark • 0
1
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2
replies
616
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
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2
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479
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
0
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2
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828
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
1
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1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 9 months ago by ▴ 20
0
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5
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3.0k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
votes
3
replies
625
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
votes
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.2 years ago by • 0
1
vote
4
replies
865
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
677
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
1
reply
544
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
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2
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771
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
2
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3
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608
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
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4
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807
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
0
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0
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427
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
8
votes
13
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1.9k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
0
replies
410
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
0
votes
1
reply
561
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Postdoctoral Position in Bioinformatics - Mainz, Germany by Jammie • 0
[Online kasiinod][1] pakuvad mängijatele võimalust nautida põnevat hasartmängukogemust otse oma arvuti või mobiilseadme kaudu. Need kasiino…
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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