Showing : Diffbind • reset
0
votes
0
replies
156
views
Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
6 weeks ago kim • 0
0
votes
0
replies
126
views
diffbind covariates
DiffBind ATACSeq
updated 7 weeks ago by 43k • written 7 weeks ago by ▴ 220
0
votes
2
replies
471
views
DiffBind dba.report discrepancy
DiffBind
9 weeks ago • updated 8 weeks ago aelbassiouny • 0
0
votes
0
replies
98
views
DiffBind subset replicates
DiffBind
9 weeks ago Haiping • 0
0
votes
0
replies
169
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
10 weeks ago Young Boqin • 0
0
votes
0
replies
220
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
3 months ago Alejandro • 0
0
votes
2
replies
362
views
DiffBind for MBD-seq
MBD-seq DiffBind
3 months ago Marianna ▴ 20
0
votes
0
replies
250
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
287
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
4 months ago mdidish ▴ 10
0
votes
0
replies
242
views
DiffBind dba.plotprofile y-axis range
DiffBind
4 months ago Tara • 0
0
votes
8
replies
739
views
DiffBind full library size not reliable
DiffBind Reads MACS2 FullLibSize
updated 4 months ago by ★ 5.2k • written 4 months ago by ▴ 20
1
vote
3
replies
488
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
377
views
Blacklist regions on DBA object (diffbind)
DiffBind chipseq
5 months ago gamma.jian ▴ 10
0
votes
2
replies
461
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind DifferentialPeakCalling
6 months ago Mallory • 0
0
votes
0
replies
259
views
Difference in Contrast in DiffBind
DiffBind
7 months ago user_bioinfo • 0
0
votes
0
replies
292
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
7 months ago Dinesh • 0
0
votes
1
reply
566
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 6 weeks ago by • 0 • written 7 months ago by ▴ 10
0
votes
0
replies
371
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
7 months ago yvonneh • 0
0
votes
0
replies
288
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
7 months ago Ian D. ▴ 70
0
votes
9
replies
1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
7 months ago • updated 9 weeks ago Ian D. ▴ 70
3
votes
1
reply
492
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 7 months ago by 43k • written 7 months ago by ▴ 10
0
votes
1
reply
737
views
ATACseq merge peaks
DiffBind
updated 7 months ago by ★ 4.6k • written 8 months ago by • 0
0
votes
4
replies
563
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
281
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
8 months ago Virangika • 0
2
votes
2
replies
611
views
[DiffBind] Obtaining normalization factors
DiffBind
8 months ago Henry ▴ 10
2
votes
2
replies
986
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
8 months ago Henry ▴ 10
0
votes
0
replies
378
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
8 months ago feather-W • 0
0
votes
0
replies
379
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
8 months ago Ankit ▴ 20
0
votes
0
replies
346
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
8 months ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
373
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
9 months ago erbrocato • 0
0
votes
2
replies
617
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 months ago Sam ▴ 10
0
votes
1
reply
471
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 months ago red_bricks ▴ 60
0
votes
1
reply
610
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
626
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
370
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
11 months ago frueher • 0
0
votes
0
replies
344
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
11 months ago Aswathy • 0
0
votes
0
replies
509
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
11 months ago Hai • 0
0
votes
0
replies
454
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
11 months ago inna.gur • 0
0
votes
1
reply
1.2k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 11 months ago by • 0 • written 16 months ago by • 0
0
votes
2
replies
635
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 12 months ago by ▴ 10
1
vote
2
replies
558
views
Inconsistent results in DiffBind
DiffBind
12 months ago Sam ▴ 10
1
vote
1
reply
603
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
0
votes
0
replies
640
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
647
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 14 months ago by 67k • written 14 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 14 months ago by • 0
2
votes
2
replies
673
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
14 months ago r.murakami • 0
1
vote
1
reply
782
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 14 months ago by 67k • written 14 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
903
views
diffbind analyze for wheat
DiffBind
updated 9 months ago by • 0 • written 15 months ago by • 0
0
votes
1
reply
843
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: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
WEHI, Melbourne, Australia, 24 minutes ago
30 N Gould St STE 39034 Sheridan, WY, 25 minutes ago
Pakistan, 1 hour ago
Germany, 4 hours ago
Barcelona/Universitat Pompeu Fabra, 4 hours ago
Traffic: 431 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