Showing : diffbind • reset
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
2 days ago Dinesh • 0
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75
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dba.plotProfile() plotting and interpretation
DiffBind
5 days ago Henry ▴ 10
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54
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
6 days ago yvonneh • 0
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50
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 days ago Ian D. ▴ 70
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3
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171
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
7 days ago • updated 12 hours ago Ian D. ▴ 70
1
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123
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 8 days ago by 42k • written 8 days ago by • 0
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1
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141
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ATACseq merge peaks
DiffBind
updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
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4
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242
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
21 days ago • updated 18 days ago lonn • 0
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96
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
23 days ago Virangika • 0
2
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2
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172
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[DiffBind] Obtaining normalization factors
DiffBind
26 days ago • updated 22 days ago Henry ▴ 10
2
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2
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393
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
27 days ago • updated 26 days ago Henry ▴ 10
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115
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
5 weeks ago feather-W • 0
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113
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
5 weeks ago Ankit ▴ 20
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101
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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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144
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
7 weeks ago erbrocato • 0
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2
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255
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago • updated 7 weeks ago Sam ▴ 10
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1
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202
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Exact same results in Diffbind with different normalization methods
DiffBind
8 weeks ago • updated 7 weeks ago red_bricks ▴ 50
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1
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304
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Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
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0
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249
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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178
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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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173
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
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0
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246
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Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
4 months ago Hai • 0
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261
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
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1
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942
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DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
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2
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358
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
1
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2
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332
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Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
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1
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360
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
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336
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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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412
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 65k • written 7 months ago by • 0
2
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4
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1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 7 months ago by • 0 • written 7 months ago by • 0
2
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2
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470
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
1
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459
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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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869
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
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3
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639
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diffbind analyze for wheat
DiffBind
updated 10 weeks ago by • 0 • written 7 months ago by • 0
0
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1
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552
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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
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636
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago Junsik • 0
0
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2
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493
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DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
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2
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849
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DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
1
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1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 20
0
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5
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3.1k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
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3
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639
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
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5
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1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.3 years ago by • 0
1
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4
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880
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago • updated 9 months ago Theo ▴ 10
1
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2
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691
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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
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1
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552
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
1
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2
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785
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Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago Chris • 0
2
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3
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622
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Sample sheet file for DiffBind
DiffBind
updated 4 months ago by • 0 • written 10 months ago by • 0
4
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4
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826
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
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0
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436
views
Help with error running DiffBind
DiffBind
11 months ago Chris • 0
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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