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diffBind
•
reset
0
votes
0
replies
90
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
12 days ago
jared.andrews07
▴ 30
0
votes
0
replies
156
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 7 weeks ago by
James W. MacDonald
64k • written 7 weeks ago by
sophie.hfliu
• 0
2
votes
4
replies
966
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 6 weeks ago by
Matt Eldridge
• 0 • written 7 weeks ago by
r.murakami
• 0
2
votes
2
replies
255
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 weeks ago
r.murakami
• 0
1
vote
1
reply
230
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 weeks ago by
James W. MacDonald
64k • written 8 weeks ago by
lin.pei26
• 0
3
votes
7
replies
514
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 10 weeks ago by
Chris
• 0
0
votes
2
replies
305
views
diffbind analyze for wheat
DiffBind
10 weeks ago
zgyu12
• 0
0
votes
1
reply
290
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
3 months ago
Mark
• 0
0
votes
0
replies
238
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
3 months ago
Mark
• 0
1
vote
2
replies
330
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
3 months ago
Junsik
• 0
0
votes
2
replies
258
views
DiffBind error
DiffBind
updated 3 months ago by
Rory Stark
★ 5.1k • written 3 months ago by
M.Vukic
• 0
0
votes
2
replies
463
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 4 months ago by
Malcolm Cook
★ 1.6k • written 4 months ago by
Nebat
• 0
1
vote
1
reply
829
views
Help with error DiffBind
DiffBind
updated 4 months ago by
Rory Stark
★ 5.1k • written 4 months ago by
Chris
• 0
0
votes
1
reply
860
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 4 months ago by
Rory Stark
★ 5.1k • written 4 months ago by
bhandary.8590
• 0
0
votes
5
replies
1.2k
views
diffbind
DiffBind
chipseq
updated 4 months ago by
Rory Stark
★ 5.1k • written 4 months ago by
ANAMIKA
• 0
0
votes
3
replies
353
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 4 months ago by
Rory Stark
★ 5.1k • written 4 months ago by
jason.kost
• 0
0
votes
5
replies
812
views
DiffBind handling of replicates and consensus
diffbind
updated 8 weeks ago by
Rory Stark
★ 5.1k • written 3.8 years ago by
Jim
• 0
0
votes
4
replies
493
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
4 months ago
Theo
• 0
1
vote
2
replies
434
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 4 months ago by
Rory Stark
★ 5.1k • written 4 months ago by
Stevie Pederson
• 0
0
votes
1
reply
311
views
DiffBind output issues
DiffBind
updated 5 months ago by
Rory Stark
★ 5.1k • written 5 months ago by
David.Atkinson2
• 0
1
vote
2
replies
439
views
Interpret plots from DiffBind
DiffBind
5 months ago
Chris
• 0
2
votes
2
replies
348
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by
steffies127
• 0 • written 5 months ago by
Chris
• 0
4
votes
4
replies
478
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
5 months ago
bhandary.8590
• 0
0
votes
0
replies
263
views
Help with error running DiffBind
DiffBind
5 months ago
Chris
• 0
1
vote
5
replies
671
views
Diffbind "No genome detected"
DiffBind
5 months ago
kyliecode
• 0
7
votes
13
replies
1.2k
views
Interpret plot from DiffBind
DiffBind
updated 5 months ago by
Rory Stark
★ 5.1k • written 6 months ago by
Chris
• 0
0
votes
0
replies
234
views
Title in dba.plotProfile
DiffBind
6 months ago
agata17
• 0
0
votes
1
reply
360
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 6 months ago by
Rory Stark
★ 5.1k • written 6 months ago by
littlefishes20
▴ 10
0
votes
1
reply
395
views
DiffBind dba() in parallel
DiffBind
updated 6 months ago by
Rory Stark
★ 5.1k • written 6 months ago by
Shashank
• 0
1
vote
4
replies
622
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 5 months ago by
Rory Stark
★ 5.1k • written 6 months ago by
lin.pei26
• 0
0
votes
0
replies
283
views
Fold values in Diffbind
DiffBind
6 months ago
bhandary.8590
• 0
2
votes
3
replies
551
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 6 months ago by
jandrade
• 0
0
votes
0
replies
306
views
Help with Diffbind result
DiffBind
6 months ago
Chris
• 0
3
votes
4
replies
1.1k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
6 months ago
Mark
• 0
0
votes
7
replies
960
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
7 months ago • updated 6 months ago
Ti
• 0
2
votes
1
reply
363
views
how diffbind count the reads of each peak in each sample?
diffbind
DiffBind
updated 7 months ago by
Rory Stark
★ 5.1k • written 7 months ago by
hfyuan2016
• 0
0
votes
5
replies
757
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 6 months ago by
householdelsewhere
• 0 • written 7 months ago by
Oscar
• 0
4
votes
6
replies
667
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
7 months ago
Chris
• 0
0
votes
1
reply
367
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 7 months ago by
Rory Stark
★ 5.1k • written 7 months ago by
bhandary.8590
• 0
0
votes
2
replies
496
views
Question regarding multiple comparisons in DiffBind
DiffBind
7 months ago
epipally
• 0
8
votes
13
replies
1.8k
views
Help with Error in DiffBind
DiffBind
ATACSeq
8 months ago
Chris
• 0
0
votes
2
replies
574
views
Multiple issues reading in peak sets with Diffbind
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
os306
• 0
0
votes
2
replies
713
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
8 months ago
Giulia
• 0
0
votes
0
replies
294
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2
ChIPSeq
DiffBind
edgeR
HistoneModification
8 months ago
Giulia
• 0
1
vote
3
replies
426
views
Using DiffBind Normalization and Contrasting on Fold Change Values
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
ssankar3
• 0
1
vote
2
replies
401
views
DiffBind spike-in lib.sizes confusion
SpikeIn
DiffBind
8 months ago
Weisheng
• 0
0
votes
13
replies
1.0k
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze
DiffBind
@rory-stark-5741
8 months ago
tahir.msajid
• 0
0
votes
1
reply
328
views
DiffBind---peak region reads or all reads?
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
skyyks123
• 0
0
votes
0
replies
267
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind
MeRIP-seq
m6A-seq
8 months ago
zhiyi
• 0
0
votes
1
reply
528
views
DiffBind differential analysis
DifferentialPeakCalling
ChIPanalyser
DiffBind
chipseqDB
updated 9 months ago by
Rory Stark
★ 5.1k • written 9 months ago by
narzouni
• 0
50 results • Page
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Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
No, I don't. Confirm that `geneList` has the expected format. What is the outcome of `geneList[1:5]`, `str(geneList)` and `class(geneList)…
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
Did you try it yourselves? But the answer is yes.
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
nromerov
• 0
Also do you know if the gaphical functions as dotplot, enrichmap and cnetplot works on this generic analysis? still sorry for bothering you
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
nromerov
• 0
Thank you very much for your help iu was really deseperate about this that i wasn't thinking too well yesterday im really gratefull with yo…
Comment: Ensembl down???
by
bas_work
▴ 20
I want to link 'external_gene_names' (mouse, multiple lists) with the ensembl gene IDs and HGNC symbols of human orthologues using getLDS()…
Votes
Answer: gseGO input list
Comment: Problem loading HDF5Array in R 4.3.2
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Ensembl down???
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