Showing : DiffBind • reset
0
votes
0
replies
166
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
7 weeks ago kim • 0
0
votes
0
replies
135
views
diffbind covariates
DiffBind ATACSeq
updated 9 weeks ago by 43k • written 9 weeks ago by ▴ 220
0
votes
2
replies
486
views
DiffBind dba.report discrepancy
DiffBind
10 weeks ago • updated 9 weeks ago aelbassiouny • 0
0
votes
0
replies
105
views
DiffBind subset replicates
DiffBind
10 weeks ago Haiping • 0
0
votes
0
replies
183
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
11 weeks ago Young Boqin • 0
0
votes
0
replies
229
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
3 months ago Alejandro • 0
0
votes
2
replies
367
views
DiffBind for MBD-seq
MBD-seq DiffBind
4 months ago Marianna ▴ 20
0
votes
0
replies
258
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
4 months ago Ian D. ▴ 70
0
votes
1
reply
298
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
4 months ago mdidish ▴ 10
0
votes
0
replies
248
views
DiffBind dba.plotprofile y-axis range
DiffBind
4 months ago Tara • 0
0
votes
8
replies
750
views
DiffBind full library size not reliable
DiffBind Reads MACS2 FullLibSize
updated 4 months ago by ★ 5.2k • written 5 months ago by ▴ 20
1
vote
3
replies
495
views
Create merged ChIP heatmap across conditions
DiffBind profileplyr
updated 5 months ago by ★ 5.2k • written 5 months ago by • 0
0
votes
0
replies
387
views
Blacklist regions on DBA object (diffbind)
DiffBind chipseq
6 months ago gamma.jian ▴ 10
0
votes
2
replies
473
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind DifferentialPeakCalling
6 months ago Mallory • 0
0
votes
0
replies
266
views
Difference in Contrast in DiffBind
DiffBind
7 months ago user_bioinfo • 0
0
votes
0
replies
297
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
7 months ago Dinesh • 0
0
votes
1
reply
578
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 7 weeks ago by • 0 • written 8 months ago by ▴ 10
0
votes
0
replies
382
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
8 months ago yvonneh • 0
0
votes
0
replies
294
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 months ago Ian D. ▴ 70
0
votes
9
replies
1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 months ago • updated 10 weeks ago Ian D. ▴ 70
3
votes
1
reply
502
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 8 months ago by 43k • written 8 months ago by ▴ 10
0
votes
1
reply
757
views
ATACseq merge peaks
DiffBind
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
votes
4
replies
572
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
8 months ago lonn • 0
0
votes
0
replies
287
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
8 months ago Virangika • 0
2
votes
2
replies
625
views
[DiffBind] Obtaining normalization factors
DiffBind
8 months ago Henry ▴ 10
2
votes
2
replies
1.0k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
8 months ago Henry ▴ 10
0
votes
0
replies
385
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
9 months ago feather-W • 0
0
votes
0
replies
386
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
9 months ago Ankit ▴ 20
0
votes
0
replies
351
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
9 months ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
380
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
9 months ago erbrocato • 0
0
votes
2
replies
626
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 months ago Sam ▴ 10
0
votes
1
reply
479
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 months ago red_bricks ▴ 60
0
votes
1
reply
627
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
11 months ago isaromero8888 • 0
0
votes
0
replies
634
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
11 months ago Jawahar • 0
0
votes
0
replies
376
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
11 months ago frueher • 0
0
votes
0
replies
349
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
11 months ago Aswathy • 0
0
votes
0
replies
516
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
12 months ago Hai • 0
0
votes
0
replies
461
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
12 months ago inna.gur • 0
0
votes
1
reply
1.3k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 12 months ago by • 0 • written 16 months ago by • 0
0
votes
2
replies
643
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 12 months ago by ▴ 10
1
vote
2
replies
562
views
Inconsistent results in DiffBind
DiffBind
12 months ago Sam ▴ 10
1
vote
1
reply
607
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
0
votes
0
replies
646
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
13 months ago jared.andrews07 ▴ 30
0
votes
0
replies
655
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 15 months ago by 67k • written 15 months ago by • 0
2
votes
4
replies
1.6k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 14 months ago by ▴ 10 • written 15 months ago by • 0
2
votes
2
replies
680
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
15 months ago • updated 14 months ago r.murakami • 0
1
vote
1
reply
789
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 15 months ago by 67k • written 15 months ago by • 0
3
votes
7
replies
1.3k
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 15 months ago by ▴ 20
0
votes
3
replies
910
views
diffbind analyze for wheat
DiffBind
updated 10 months ago by • 0 • written 15 months ago by • 0
0
votes
1
reply
848
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
16 months ago Mark • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to rohitsatyam102 ▴ 20
Popular Question to Hervé Pagès 16k
Teacher to dsull ▴ 40
Popular Question to bpshtiwan ▴ 10
Locations • All
India, 30 minutes ago
Sweden, 50 minutes ago
UPF, Barcelona, Spain, 1 hour ago
Pakistan, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 428 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