Showing : DiffBind • reset
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
2 days ago Dinesh • 0
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82
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dba.plotProfile() plotting and interpretation
DiffBind
6 days ago Henry ▴ 10
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59
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
7 days ago yvonneh • 0
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55
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 days ago Ian D. ▴ 70
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3
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188
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 days ago • updated 1 day ago Ian D. ▴ 70
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130
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 9 days ago by 42k • written 9 days ago by • 0
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1
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142
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ATACseq merge peaks
DiffBind
updated 13 days ago by ★ 4.1k • written 15 days ago by • 0
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4
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244
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
22 days ago • updated 19 days ago lonn • 0
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97
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
23 days ago Virangika • 0
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2
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173
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[DiffBind] Obtaining normalization factors
DiffBind
27 days ago • updated 23 days ago Henry ▴ 10
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2
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395
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
28 days ago • updated 27 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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114
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
5 weeks ago Ankit ▴ 20
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102
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
6 weeks ago Pierre Lindenbaum ▴ 10
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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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257
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 weeks ago Sam ▴ 10
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1
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203
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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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308
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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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252
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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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179
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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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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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248
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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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264
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ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
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2
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333
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Inconsistent results in DiffBind
DiffBind
5 months ago • updated 4 months ago Sam ▴ 10
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2
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361
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
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1
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361
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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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337
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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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2
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470
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 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
1
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1
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460
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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
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3
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640
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diffbind analyze for wheat
DiffBind
updated 10 weeks ago by • 0 • written 7 months ago by • 0
3
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7
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871
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
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1
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554
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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
0
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1
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943
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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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493
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DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
1
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2
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637
views
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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3
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641
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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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2
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851
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
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
1
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1
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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
1
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4
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882
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diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago Theo ▴ 10
1
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2
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693
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
1
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1
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1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
2
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3
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630
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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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828
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
1
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2
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788
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Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago Chris • 0
0
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1
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553
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
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0
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436
views
Help with error running DiffBind
DiffBind
11 months ago Chris • 0
1
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7
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1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma by Shaimaa Gamal • 0
I have performed RUVg correction and extracted W, factors of unwanted variation. According to limma guide, > In the limma approach to RNA…
Comment: DSS CpG coverage threshold by j.gilbert • 0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says: *Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
I'll take a look later. For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
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