Showing : diffbind • reset
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69
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Difference in Contrast in DiffBind
DiffBind
13 days ago zzrammal • 0
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0
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111
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
22 days ago Dinesh • 0
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0
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134
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dba.plotProfile() plotting and interpretation
DiffBind
25 days ago Henry ▴ 10
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105
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
26 days ago yvonneh • 0
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0
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100
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
26 days ago Ian D. ▴ 70
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5
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437
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
27 days ago • updated 4 days ago Ian D. ▴ 70
1
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1
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166
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 28 days ago by 42k • written 28 days ago by • 0
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1
reply
191
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ATACseq merge peaks
DiffBind
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by • 0
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4
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283
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
5 weeks ago lonn • 0
0
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0
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114
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
6 weeks ago Virangika • 0
2
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2
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202
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[DiffBind] Obtaining normalization factors
DiffBind
6 weeks ago Henry ▴ 10
2
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2
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434
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
6 weeks ago Henry ▴ 10
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0
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129
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
8 weeks ago feather-W • 0
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0
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132
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
8 weeks ago Ankit ▴ 20
0
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0
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118
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
8 weeks ago Pierre Lindenbaum ▴ 10
0
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0
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159
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
9 weeks ago erbrocato • 0
0
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2
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285
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
11 weeks ago • updated 10 weeks ago Sam ▴ 10
0
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1
reply
225
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Exact same results in Diffbind with different normalization methods
DiffBind
11 weeks ago • updated 10 weeks ago red_bricks ▴ 50
0
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1
reply
337
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
4 months ago isaromero8888 • 0
0
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0
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282
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
4 months ago Jawahar • 0
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0
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197
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
4 months ago frueher • 0
0
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0
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189
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago Aswathy • 0
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0
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277
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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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0
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285
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
5 months ago inna.gur • 0
0
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1
reply
965
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 5 months ago by • 0 • written 9 months ago by • 0
0
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2
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386
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
1
vote
2
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359
views
Inconsistent results in DiffBind
DiffBind
5 months ago Sam ▴ 10
1
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1
reply
384
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DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
0
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0
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357
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
0
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0
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439
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 66k • written 7 months ago by • 0
2
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4
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1.3k
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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494
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
1
vote
1
reply
482
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 8 months ago by 66k • written 8 months ago by • 0
3
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7
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920
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
0
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3
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671
views
diffbind analyze for wheat
DiffBind
updated 3 months ago by • 0 • written 8 months ago by • 0
0
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1
reply
578
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
9 months ago Mark • 0
1
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2
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669
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago Junsik • 0
0
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2
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517
views
DiffBind error
DiffBind
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
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2
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891
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 10 months ago by ★ 1.6k • written 10 months ago by • 0
1
vote
1
reply
2.1k
views
Help with error DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by ▴ 10
1
vote
1
reply
2.4k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 10 months ago by ★ 5.2k • written 10 months ago by ▴ 20
0
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5
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3.4k
views
diffbind
DiffBind chipseq
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
3
replies
696
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
5
replies
1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 8 months ago by ★ 5.2k • written 4.3 years ago by • 0
1
vote
4
replies
920
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago Theo ▴ 10
1
vote
2
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727
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
574
views
DiffBind output issues
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
1
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2
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853
views
Interpret plots from DiffBind
DiffBind
11 months ago Chris ▴ 10
2
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3
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659
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
4
votes
4
replies
860
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
11 months ago bhandary.8590 ▴ 20
50 results • Page 1 of 1
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Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contr…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…
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I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…
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Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.
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See https://support.bioconductor.org/p/9158324/#9158336 . We have reached out to goseq to fix the package; we have a community member …
Votes
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
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