Showing : diffBind • reset
0
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5
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CHIP Seq Analysis by DiffBind Package
DiffBind ChIPchip
updated 5.0 years ago by ★ 5.2k • written 5.1 years ago by • 0
0
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7
replies
2.7k
views
Error report when loading a 0-byte bed file for DBA object in Diffbind
DiffBind
5.1 years ago • updated 5.0 years ago ahua217 ▴ 10
0
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10
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2.9k
views
Error report when using dab() in Diffbind
DiffBind
5.2 years ago • updated 5.1 years ago ahua217 ▴ 10
0
votes
5
replies
2.1k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind Genrich
updated 2.6 years ago by • 0 • written 5.2 years ago by • 0
0
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3
replies
1.3k
views
DiffBind reporting error
DiffBind
updated 4.7 years ago by ★ 5.2k • written 5.2 years ago by • 0
2
votes
2
replies
3.1k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
5.2 years ago • updated 4.9 years ago Mar Mar ▴ 20
4
votes
5
replies
2.4k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 8.3 years ago by ▴ 30
0
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3
replies
1.4k
views
Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbind normalization
updated 5.2 years ago by ★ 5.2k • written 9.5 years ago by • 0
0
votes
2
replies
1.5k
views
DiffBind PE data
diffbind paired-end reads
updated 5.2 years ago by ★ 5.2k • written 9.0 years ago by ▴ 60
1
vote
4
replies
2.3k
views
Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 10 months ago by • 0 • written 7.4 years ago by ▴ 10
0
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2
replies
2.3k
views
DiffBind with highly variable FRiP (Fraction Reads in Peaks)
DiffBind
updated 5.2 years ago by ★ 5.2k • written 6.9 years ago by ▴ 20
2
votes
5
replies
1.7k
views
how to get the estimated libSize in DiffBind
diffbind
updated 5.2 years ago by ★ 5.2k • written 5.6 years ago by ▴ 40
1
vote
2
replies
1.0k
views
Can I completely repeat the DiffBind results using DESeq2?
diffbind
updated 5.2 years ago by ★ 5.2k • written 5.6 years ago by ▴ 40
1
vote
2
replies
1.2k
views
Using multiple covariates in DIffBind
DiffBind Deseq2
updated 5.2 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
1
vote
4
replies
2.7k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 5.2 years ago by ★ 5.2k • written 8.0 years ago by • 0
2
votes
4
replies
2.4k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 5.2 years ago by ★ 5.2k • written 6.2 years ago by ▴ 40
1
vote
8
replies
2.2k
views
Diffbind multiple blocking factor
diffbind rory stark chip seq
updated 5.2 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Diffbind multiple groups
diffbind
updated 5.2 years ago by ★ 5.2k • written 6.9 years ago by ▴ 160
4
votes
3
replies
1.6k
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 5.2 years ago by ★ 5.2k • written 6.2 years ago by ▴ 10
0
votes
3
replies
1.8k
views
DiffBind custom normalization factor
diffbind
updated 9 months ago by • 0 • written 5.8 years ago by ▴ 140
0
votes
2
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1.4k
views
Diffbind with multiple blocking factors
diffbind blocking model
updated 5.2 years ago by ★ 5.2k • written 6.2 years ago by ▴ 10
1
vote
3
replies
4.0k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 5.2 years ago by ★ 5.2k • written 7.9 years ago by ▴ 10
1
vote
1
reply
2.3k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.2 years ago by ★ 5.2k
1
vote
1
reply
2.3k
views
DiffBind for ATAC-Seq count extraction
esATAC edgeR DiffBind
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by • 0
1
vote
10
replies
4.0k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by ▴ 70
4
votes
8
replies
3.5k
views
How DiffBind run PCA based on peak data?
DiffBind
updated 5.2 years ago by ★ 5.2k • written 8.3 years ago by ▴ 20
1
vote
2
replies
1.2k
views
diffbind error in sum(sapply(peaks, nrow)) : invalid 'type' (list) of argument
diffbind
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by • 0
2
votes
2
replies
1.6k
views
[dba.plotvenn] Can I move around the numbers in the diagram so that they fit inside the overlapped region?
diffbind plot venn diagram
updated 5.2 years ago by ★ 5.2k • written 5.2 years ago by • 0
1
vote
1
reply
1.4k
views
Error in dba.count and dba.analyze
DiffBind chip-seq differentially-binding-site
updated 5.3 years ago by ★ 5.2k • written 5.3 years ago by ▴ 20
1
vote
5
replies
1.9k
views
is it possible to analysis with more than 5 treatment with dba.overlap?
diffbind
updated 5.2 years ago by • 0 • written 5.3 years ago by ▴ 10
0
votes
0
replies
854
views
How can I extract the information inside the heatmap of peak by dba.plotHeatmap
diffbind
5.4 years ago qq809825706 ▴ 10
2
votes
7
replies
2.2k
views
can the counts extracted from Diffbind be used to analysis in Deseq2 as the RNAseq?
deseq2 diffbind
updated 3.7 years ago by ★ 5.2k • written 5.4 years ago by ▴ 10
0
votes
2
replies
2.2k
views
DiffBind consensus peak set
DiffBind MACS2
updated 5.4 years ago by ★ 5.2k • written 5.4 years ago by • 0
3
votes
7
replies
2.3k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 30
2
votes
1
reply
833
views
diffbind from own binding affinity table
diffbind R
updated 5.4 years ago by ★ 5.2k • written 5.4 years ago by • 0
0
votes
2
replies
1.8k
views
ChIP-seq MA plot possibly skewed - how to normalise?
DiffBind MA plot normalization ChIP-seq
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
2
votes
2
replies
1.5k
views
Cannot install DiffBind on R3.5 due to amap dependency
DiffBind ama
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
2
votes
7
replies
2.1k
views
Deferentially binding site is the same for all the samples
chip-seq diffBind sequence_analysis
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by ▴ 20
0
votes
1
reply
2.4k
views
DiffBind Error Processing one or more read files
diffbind 3.5.1 3.6.1
updated 5.5 years ago by ★ 5.2k • written 5.6 years ago by • 0
0
votes
4
replies
2.6k
views
DiffBind or csaw between different transcription factors
DiffBind csaw
updated 5.6 years ago by ★ 29k • written 5.6 years ago by ▴ 20
0
votes
1
reply
908
views
Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
DiffBind ChIP-seq
updated 5.6 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
0
votes
1
reply
2.0k
views
use diffbind with normilized bedgraph files from spike ins
diffbind chip-seq chip spike spike-ins
updated 5.6 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
0
votes
1
reply
673
views
DiffBind count() error or it crashes R Studio
diffbind
updated 5.6 years ago by ★ 5.2k • written 5.8 years ago by • 0
1
vote
8
replies
3.6k
views
Extracting raw read counts in DiffBind consensus peak set
DiffBind
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by • 0
1
vote
3
replies
1.8k
views
DiffBind: reverse absolute fold change in dba.report ie. abs(rep$Fold)
diffbind atac
updated 5.7 years ago by ★ 5.2k • written 5.7 years ago by • 0
2
votes
2
replies
882
views
DESeq2 for ChIP/CLIP-seq: one-sided test
deseq2 diffbind
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
4
replies
1.7k
views
remove background color from dba.plotVolcano (Diffbind)
diffbind
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
1
vote
2
replies
1.4k
views
The coordinate system problem about DiffBind output
diffbind Rory Stark coordinate
updated 5.8 years ago by ★ 5.2k • written 5.9 years ago by ▴ 40
3
votes
2
replies
1.4k
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind CPM TMM
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 40
1
vote
2
replies
796
views
Diffbind- results different every time I run it
software error DiffBind
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by • 0
679 results • Page 6 of 14
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Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
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