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Showing :
atacseq
•
reset
8
votes
13
replies
2.8k
views
Help with Error in DiffBind
DiffBind
ATACSeq
13 months ago
Chris
• 0
5
votes
8
replies
2.2k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 23 months ago by
Johanna Hardin
▴ 20 • written 2.8 years ago by
pegah.taklifi
▴ 30
5
votes
8
replies
1.0k
views
Help with error install csaw
ChIPSeq
ATACSeq
written 13 months ago by
Chris
• 0
4
votes
6
replies
928
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
12 months ago
Chris
• 0
3
votes
5
replies
861
views
How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by
James W. MacDonald
65k • written 13 months ago by
Chris
• 0
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.1 years ago by
pgontarz
▴ 10
2
votes
4
replies
1.4k
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 5.6 years ago by
Rory Stark
★ 5.2k • written 5.6 years ago by
gtechbio
▴ 10
2
votes
5
replies
3.3k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 16 months ago by
Junsik
• 0 • written 2.9 years ago by
Rory Stark
★ 5.2k
2
votes
1
reply
1.6k
views
DiffBind on ATAC seq data
ATACSeq
updated 13 months ago by
Rory Stark
★ 5.2k • written 13 months ago by
Chris
• 0
2
votes
4
replies
1.6k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
updated 3.2 years ago by
Rory Stark
★ 5.2k • written 3.2 years ago by
Asma
• 0
2
votes
3
replies
959
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
2.0 years ago • updated 23 months ago
bers.anthrope
• 0
2
votes
5
replies
4.4k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 20 months ago by
eric.kern13
▴ 20 • written 2.6 years ago by
changxu.fan
▴ 20
1
vote
3
replies
1.5k
views
Using block and design together in Diffbind 3.0?
DiffBind
R
ATACSeq
updated 2.8 years ago by
sbcn
▴ 80 • written 2.8 years ago by
fleur_p90
• 0
1
vote
1
reply
1.5k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 3.5 years ago by
Rory Stark
★ 5.2k
1
vote
3
replies
1.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 5 months ago by
dineika.chandrananda
• 0 • written 2.0 years ago by
zgraytho88
• 0
1
vote
5
replies
1.7k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind
ATACSeq
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
fleur_p90
• 0
1
vote
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 3.5 years ago by
Rory Stark
★ 5.2k • written 3.5 years ago by
CodeAway
▴ 70
1
vote
2
replies
2.0k
views
DeSEQ2- What is the difference between Gene Clustering and using LRT for Time Series experiment WITHOUT treatments
deseq2
Time Series
Gene Clustering
LRT
ATACseq
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
kaiser.karim
• 0
1
vote
2
replies
9.3k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.7 years ago by
Ou, Jianhong
★ 1.3k • written 3.7 years ago by
Arpi Beshlikyan
• 0
1
vote
4
replies
1.5k
views
Binding matrix created by DiffBind
ATACSeq
DiffBind
2.9 years ago
sh.kazempour94
▴ 10
0
votes
2
replies
1.2k
views
mogsa on RNA-seq and ATAC-seq data
mogsa
atacseq
updated 5.9 years ago by
mengchen18
• 0 • written 5.9 years ago by
meeta.mistry
▴ 30
0
votes
0
replies
256
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
4 months ago
inna.gur
• 0
0
votes
2
replies
1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
5.0 years ago
tangming2005
▴ 190
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 4.9 years ago by
Steve Lianoglou
★ 13k • written 4.9 years ago by
mbasam
• 0
0
votes
4
replies
1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 3.7 years ago by
Ou, Jianhong
★ 1.3k • written 3.7 years ago by
achaillon
• 0
0
votes
4
replies
230
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 13 days ago
lonn
• 0
0
votes
1
reply
658
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 14 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
Hadar
• 0
0
votes
4
replies
1.3k
views
DiffBind
ATACSeq
DiFFBind
3.0 years ago
Riba Michela
▴ 90
0
votes
7
replies
653
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 8 weeks ago by
danalvoronov
▴ 10 • written 5 months ago by
jfmay
• 0
0
votes
0
replies
720
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
21 months ago
Sebastian Lewandowski
• 0
0
votes
1
reply
562
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 15 months ago by
Ou, Jianhong
★ 1.3k • written 15 months ago by
tahir.msajid
• 0
0
votes
0
replies
244
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
0
votes
1
reply
1.3k
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 22 months ago by
Rory Stark
★ 5.2k • written 22 months ago by
young
• 0
0
votes
2
replies
833
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 9 months ago by
Malcolm Cook
★ 1.6k • written 9 months ago by
Nebat
• 0
0
votes
0
replies
406
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sophie.hfliu
• 0
0
votes
0
replies
572
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq
ATACseq
sample-size
17 months ago
gogniu
• 0
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
updated 20 months ago by
Rory Stark
★ 5.2k • written 2.6 years ago by
adR
▴ 30
0
votes
1
reply
298
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
3 months ago
isaromero8888
• 0
0
votes
0
replies
582
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
2.1 years ago
hyjforesight
• 0
0
votes
2
replies
1.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 8 months ago by
Noah
• 0 • written 20 months ago by
Taeim
• 0
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
41 results • Page
1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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