Showing : DiffBind • reset
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33
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Difference in Contrast in DiffBind
DiffBind
3 days ago zzrammal • 0
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0
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88
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need help with Diffbind multiple groups
DiffBind ChIPSeqData
11 days ago Dinesh • 0
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117
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dba.plotProfile() plotting and interpretation
DiffBind
14 days ago Henry ▴ 10
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89
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
15 days ago yvonneh • 0
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84
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago Ian D. ▴ 70
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4
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367
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 days ago by • 0 • written 17 days ago by ▴ 70
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155
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
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1
reply
170
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ATACseq merge peaks
DiffBind
updated 21 days ago by ★ 4.1k • written 23 days ago by • 0
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4
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263
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 28 days ago lonn • 0
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105
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
4 weeks ago Virangika • 0
2
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2
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190
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[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago Henry ▴ 10
2
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2
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416
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 weeks ago Henry ▴ 10
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124
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
7 weeks ago feather-W • 0
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121
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
7 weeks ago Ankit ▴ 20
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109
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
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150
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Multifactor analysis in DiffBind
DiffBind multifactoranalysis
8 weeks ago erbrocato • 0
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2
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272
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Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago Sam ▴ 10
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1
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213
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Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago • updated 8 weeks ago red_bricks ▴ 50
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1
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327
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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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267
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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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0
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189
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
4 months ago frueher • 0
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183
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Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago Aswathy • 0
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269
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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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280
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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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958
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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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377
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In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
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2
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349
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Inconsistent results in DiffBind
DiffBind
5 months ago Sam ▴ 10
1
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1
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374
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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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348
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
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426
views
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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1.3k
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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484
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
1
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1
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472
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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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882
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Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
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3
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656
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diffbind analyze for wheat
DiffBind
updated 11 weeks ago by • 0 • written 8 months ago by • 0
0
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1
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566
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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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656
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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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508
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DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 9 months ago by • 0
0
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2
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875
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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
vote
1
reply
2.0k
views
Help with error DiffBind
DiffBind
updated 9 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 9 months ago by ★ 5.2k • written 10 months ago by ▴ 20
0
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5
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3.2k
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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673
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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906
views
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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709
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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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563
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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822
views
Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago Chris ▴ 10
2
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3
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652
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
4
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4
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846
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
11 months ago • updated 10 months ago bhandary.8590 ▴ 20
50 results • Page 1 of 1
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Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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