Showing : DiffBind • reset
0
votes
3
replies
82
views
DiffBind: 0 consensus peaks for dba.peakset: New bug / undocumented change introduced between version 2.14 and 3.4.11
DiffBind
updated 2 days ago by ★ 4.4k • written 3 days ago by • 0
2
votes
5
replies
118
views
Diffbind dba$binding slot finding Chr21 for an MM10 dataset
DiffBind
updated 1 day ago by • 0 • written 7 days ago by • 0
0
votes
3
replies
93
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 7 days ago by ★ 4.4k • written 8 days ago by • 0
0
votes
2
replies
98
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
updated 7 days ago by ★ 4.4k • written 28 days ago by • 0
0
votes
1
reply
143
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 6 weeks ago by ★ 4.4k • written 10 weeks ago by • 0
0
votes
0
replies
75
views
DiffBind does not load samples
DiffBind
6 weeks ago nw416 • 0
3
votes
5
replies
609
views
Retrieve loadings/eigenvalues for PCAs using DiffBind's dba.plotPCA
DiffBind dba.plotPCA
updated 6 weeks ago by ★ 4.4k • written 12 months ago by ▴ 10
1
vote
1
reply
152
views
DiffBind drop out some peaks
DiffBind
updated 6 weeks ago by ★ 4.4k • written 7 weeks ago by • 0
0
votes
0
replies
64
views
Creating a consensus peakset in DiffBind for all the conditions of an experiment
DiffBind
6 weeks ago Sam ▴ 10
1
vote
2
replies
206
views
BiocParallel error when running DiffBind
BiocParallel BiocPa DiffBind
updated 6 weeks ago by 25k • written 11 weeks ago by ▴ 10
0
votes
0
replies
85
views
DiffBind error
DiffBind DifferentialPeakCalling
9 weeks ago Amandeep • 0
0
votes
1
reply
138
views
DiffBind contrast design - pairwise with independent filtering
DiffBind
updated 10 days ago by • 0 • written 9 weeks ago by • 0
0
votes
9
replies
968
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
18 months ago • updated 3 months ago Tongjun • 0
5
votes
6
replies
316
views
How to get 3/4 peak overlap in DiffBind?
DiffBind
3 months ago Krista • 0
3
votes
11
replies
1.4k
views
How to get all possible comparisons in DiffBind
diffbind
updated 3 months ago by ★ 4.4k • written 3.4 years ago by • 0
0
votes
2
replies
308
views
dba.count() error when re-centering peaks
DiffBind
3 months ago Mark • 0
0
votes
2
replies
186
views
`dbs.all` object in the vignette
DiffBind
3 months ago Mark • 0
1
vote
6
replies
521
views
dba.count error
DiffBind
updated 3 months ago by ★ 4.4k • written 3 months ago by ▴ 10
0
votes
1
reply
107
views
DiffBind issue: zero values for all peaks in one chromosome
DiffBind
updated 3 months ago by ★ 4.4k • written 3 months ago by • 0
1
vote
6
replies
436
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind dba.count
updated 3 months ago by ★ 4.4k • written 4 months ago by • 0
2
votes
3
replies
250
views
Not able to replicated Diffbind example dataset.
DiffBind
4 months ago Ayyappa ▴ 10
0
votes
0
replies
103
views
Not able to replicated Diffbind example dataset.
DiffBind
4 months ago Ayyappa ▴ 10
1
vote
10
replies
530
views
DiffBind: Values of Called1 and Called2 do not appear to coincide with input peaks
DiffBind
updated 4 months ago by ★ 4.4k • written 4 months ago by • 0
1
vote
1
reply
242
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 4 months ago by ★ 4.4k • written 5 months ago by • 0
0
votes
7
replies
960
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 3 days ago by ★ 4.4k • written 9 months ago by • 0
0
votes
1
reply
292
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 4 months ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
229
views
diffbind binding affinity matrix
diffbind DiffBind
updated 5 months ago by ★ 4.4k • written 6 months ago by • 0
0
votes
1
reply
766
views
DiffBind bUseSummarizeOverlaps error - the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExper…
DiffBind ChIPSeqData
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
3
votes
4
replies
358
views
dba.contrast in DiffBind
v3.4.0 DiffBind
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
1
vote
2
replies
319
views
How to include/show/add correction factors/numbers to the Diffbind heat map tiles
DiffBind
updated 6 months ago by ▴ 40 • written 6 months ago by • 0
3
votes
4
replies
1.2k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 7 months ago by ▴ 10 • written 3.8 years ago by ▴ 10
0
votes
0
replies
180
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
7 months ago Drew • 0
1
vote
2
replies
275
views
DiffBind in Bioconda
DiffBind Bioconda Versions
7 months ago Riba Michela ▴ 90
0
votes
0
replies
195
views
DiffBind dba.counts memory issue
DiffBind
7 months ago rreese2 • 0
0
votes
2
replies
303
views
how to select specific genes from heatmap of differentially accessible regions of ATAC-seq in DiffBind
DiffBind
updated 7 months ago by ★ 4.4k • written 8 months ago by • 0
0
votes
1
reply
238
views
Can DiffBind do differential analysis for un-paired peaksets?
DiffBind
updated 8 months ago by ★ 4.4k • written 8 months ago by • 0
0
votes
2
replies
492
views
Diffbind dba.plotProfile attempt to select less than one element in OneIndex
DiffBind
8 months ago bhanratt • 0
0
votes
3
replies
345
views
DiifBind_DBA_report
DiffBind
updated 5 months ago by ★ 4.4k • written 8 months ago by ▴ 90
2
votes
1
reply
301
views
Diffbind: differences between design vs no design (same comparison)?
DiffBind
updated 8 months ago by ★ 4.4k • written 8 months ago by • 0
1
vote
2
replies
270
views
DiffBind fold parameter vs. IfcThreshold in DESeq2
DiffBind
8 months ago Shuwan ▴ 10
3
votes
4
replies
536
views
DiffBind (Error in if (DBA$config$parallelPackage))
parallel R DiffBind
updated 5 months ago by ★ 4.4k • written 8 months ago by • 0
0
votes
3
replies
246
views
DiffBind Occupancy analysis
DiffBind
updated 8 months ago by ★ 4.4k • written 9 months ago by • 0
1
vote
3
replies
391
views
issue with DiffBind dba.count
bam bai DiffBind dba.count Diffbind
updated 8 months ago by ★ 4.4k • written 9 months ago by ▴ 10
0
votes
0
replies
157
views
Diffbind issue
DiffBind
9 months ago mtsompana ▴ 10
3
votes
12
replies
1.0k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 9 months ago by ★ 4.4k • written 2.7 years ago by ▴ 20
0
votes
0
replies
220
views
DiffBind error during normalization
DiffBind
9 months ago jseg ▴ 10
0
votes
2
replies
274
views
DiffBind
bflip dba.report DiffBind
9 months ago • updated 8 months ago Riba Michela ▴ 90
2
votes
3
replies
418
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 8 months ago by ▴ 20 • written 9 months ago by • 0
1
vote
3
replies
391
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 10 months ago by ▴ 70 • written 10 months ago by • 0
0
votes
0
replies
193
views
Diffbind without replicates
DiffBind
10 months ago Danielle • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Yang Shi • 0
Got that sir, thanks so much!
Comment: UniprotKB AC/ID to Entrez ID Conversion by Guido Hooiveld ★ 3.2k
No, no need to modify `up`. It somehow has to do with the R.BioC version; it works when using the latest versions (R-4.2.0/BioC-3.15), but…
Comment: UniprotKB AC/ID to Entrez ID Conversion by tom.kloter • 0
Thanks a lot for your response! I tried the code in my script and got to the following result: ``` > up <- UniProt.ws(taxId=9606) > up "U…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Guido Hooiveld ★ 3.2k
Regarding the normalization method (SCAN); I have only used RMA for the reasons James explained in one of your other threads (https://suppo…
Answer: UniprotKB AC/ID to Entrez ID Conversion by Guido Hooiveld ★ 3.2k
The key to realize is that your input is a vector of Uniprot **ID**s (also known as 'entry names') . The central identifier in the Uniprot …
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
A: coefficient not estimable (limma warning)
Awards • All
Scholar to Guido Hooiveld ★ 3.2k
Scholar to Kevin Blighe 3.5k
Scholar to SamGG ▴ 270
Prophet to johnmcma ▴ 10
Popular Question to Bogdan ▴ 640
Locations • All
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia, 1 minute ago
Switzerland, 2 minutes ago
Tunisia, 8 minutes ago
Zheng Zhou, 19 minutes ago
France, 28 minutes ago
Traffic: 433 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6