Showing : DiFFBind • reset
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 6.5 years ago by ★ 5.1k • written 8.1 years ago by ▴ 60
12
votes
6
replies
4.6k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind Histone Chip-Seq Summit size
updated 23 months ago by ★ 5.1k • written 6.6 years ago by ▴ 40
8
votes
20
replies
4.6k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 2.3 years ago by ★ 5.1k • written 3.3 years ago by ▴ 10
8
votes
13
replies
2.7k
views
Help with Error in DiffBind
DiffBind ATACSeq
13 months ago • updated 12 months ago Chris • 0
7
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
7
votes
6
replies
6.8k
views
Diffbind - What exactly is a "consensus" peak set?
peakset diffbind
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by • 0
6
votes
6
replies
2.9k
views
Score column for DiffBind::dba.peakset
DiffBind chipseq
updated 9.0 years ago by ▴ 650 • written 9.0 years ago by • 0
6
votes
8
replies
2.4k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.3 years ago by • 0 • written 6.5 years ago by ▴ 60
6
votes
6
replies
4.5k
views
DiffBind merging and consensus peaks
diffbind
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by • 0
5
votes
19
replies
5.8k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by • 0 • written 2.7 years ago by ▴ 10
5
votes
9
replies
1.9k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2 diffbind basemean summarizedexperiment
5.7 years ago rbronste ▴ 60
5
votes
7
replies
3.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 2.7 years ago by ★ 5.1k • written 8.5 years ago by ▴ 20
5
votes
6
replies
3.2k
views
Checking/updating package versions
DiffBind
3.3 years ago bertb • 0
5
votes
6
replies
1.4k
views
How to get 3/4 peak overlap in DiffBind?
DiffBind
2.2 years ago Krista • 0
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 22 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
5
votes
10
replies
1.8k
views
Learning DiffBind - some basic questions
DiffBind
updated 3.1 years ago by ★ 5.1k • written 3.3 years ago by ▴ 10
5
votes
17
replies
1.8k
views
DiffBind : More fragment sizes than libraries
diffbind
updated 6.9 years ago by ★ 5.1k • written 6.9 years ago by ▴ 40
5
votes
16
replies
4.5k
views
Exporting dba.count result as a data frame
diffbind
9.0 years ago mm2489 ▴ 10
4
votes
8
replies
2.2k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind ChIPQC
8.2 years ago JD ▴ 10
4
votes
3
replies
986
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 3.5 years ago by ★ 5.1k • written 4.5 years ago by ▴ 10
4
votes
11
replies
3.3k
views
How to get all possible comparisons in DiffBind
diffbind
updated 2.2 years ago by ★ 5.1k • written 5.3 years ago by ▴ 10
4
votes
1
reply
1.8k
views
Counting Raw Reads with DiffBind
diffbind
updated 8.5 years ago by ▴ 650 • written 8.5 years ago by • 0
4
votes
7
replies
2.5k
views
Normalization in DiffBind for Atac-seq
DiffBind
3.4 years ago Debayan ▴ 20
4
votes
5
replies
1.1k
views
diffBind: differentially bound sites are highly different between using EDGER and DESEQ2
diffbind
updated 4.7 years ago by ★ 5.1k • written 4.7 years ago by • 0
4
votes
4
replies
790
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
4
votes
7
replies
2.5k
views
Diffbind dba.analyze Error in d$span : $ operator is invalid for atomic vectors
diffbind
updated 13 months ago by • 0 • written 9.1 years ago by ▴ 10
4
votes
5
replies
1.8k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.6 years ago by ▴ 30
4
votes
7
replies
2.9k
views
DiffBind how to retrieve normalized count matrix of ATAC-seq data
DiffBind
updated 3.0 years ago by ★ 5.1k • written 3.1 years ago by ▴ 10
4
votes
2
replies
2.4k
views
diffBind correlation plot
diffbind
9.0 years ago yijing.su • 0
4
votes
6
replies
898
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
12 months ago Chris • 0
3
votes
4
replies
2.3k
views
DiffBind: error with dba(sampleSheet="samples.csv")
R DiffBind
updated 7.2 years ago by ★ 5.1k • written 7.2 years ago by • 0
3
votes
2
replies
860
views
Some confuse about the DBA_SCORE_TMM_READS_EFFECTIVE_CPM in DiffBind
diffbind CPM TMM
updated 4.1 years ago by ★ 5.1k • written 4.1 years ago by ▴ 40
3
votes
12
replies
3.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.7 years ago by ★ 5.1k • written 4.6 years ago by ▴ 20
3
votes
4
replies
690
views
DiffBind block not working for me
diffbind
updated 4.5 years ago by ★ 5.1k • written 4.5 years ago by • 0
3
votes
7
replies
1.5k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 3.7 years ago by 65k • written 3.7 years ago by ▴ 30
3
votes
4
replies
2.1k
views
Can I input peak files from Genrich as input reads in DiffBind?
DiffBind Genrich
updated 5.1 years ago by ★ 5.1k • written 5.1 years ago by • 0
3
votes
5
replies
1.4k
views
News: sorted the results of function dba.report in DiffBind R package
diffbind News
updated 5.4 years ago by ★ 5.1k • written 5.4 years ago by • 0
3
votes
6
replies
1.1k
views
Possible bug at DiffBind-edgeR interface
DiffBind edgeR
updated 9.0 years ago by ★ 5.1k • written 9.0 years ago by ★ 28k
3
votes
9
replies
3.5k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 7.2 years ago by ★ 5.1k • written 7.2 years ago by ▴ 60
3
votes
7
replies
3.7k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
3
votes
3
replies
4.1k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
6.0 years ago maria.kondili ▴ 10
3
votes
5
replies
2.5k
views
Work with GRanges objects in DiffBind
diffbind
updated 7.7 years ago by ▴ 10 • written 8.7 years ago by • 0
3
votes
3
replies
1.9k
views
DiffBind : How is computed the correlation reported when using dba()
diffbind
8.9 years ago Pierre-François Roux • 0
3
votes
7
replies
2.0k
views
dba.count with pre-defined regions
dba.count dba chipseq diffbind
updated 6.4 years ago by ★ 5.1k • written 6.4 years ago by ▴ 10
3
votes
3
replies
1.4k
views
Differential analysis of multiple samples with different time points
diffbind R atac-seq
updated 5.5 years ago by ★ 5.1k • written 5.5 years ago by • 0
3
votes
4
replies
2.4k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 2.5 years ago by ▴ 10 • written 5.7 years ago by ▴ 10
3
votes
9
replies
2.1k
views
retreiving peak caller fold enrichments after generating consensus peakset in DiffBind
diffbind
updated 9.0 years ago by ★ 5.1k • written 9.0 years ago by ▴ 10
3
votes
9
replies
2.6k
views
Error When using dba.count() in DiffBind
dba.count atac-seq diffbind
updated 6.4 years ago by ▴ 650 • written 6.5 years ago by • 0
3
votes
16
replies
4.3k
views
DiffBind differential binding normalization with different levels of binding
diffbind
updated 8.6 years ago by ★ 5.1k • written 8.6 years ago by ▴ 40
3
votes
6
replies
3.6k
views
dba.count error in DiffBind
diffbind
updated 7.8 years ago by ★ 5.1k • written 7.8 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: Different Shrunk Log2FC according with reference by Michael Love 41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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