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ATACseq
•
reset
0
votes
0
replies
28
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
1 day ago
jfmay
• 0
0
votes
0
replies
158
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 7 weeks ago by
James W. MacDonald
64k • written 7 weeks ago by
sophie.hfliu
• 0
0
votes
2
replies
471
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 4 months ago by
Malcolm Cook
★ 1.6k • written 4 months ago by
Nebat
• 0
4
votes
6
replies
672
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
7 months ago
Chris
• 0
5
votes
8
replies
719
views
Help with error install csaw
ChIPSeq
ATACSeq
updated 8 months ago by
nekisaf309
• 0 • written 8 months ago by
Chris
• 0
3
votes
5
replies
651
views
How to annotate genes from results of DiffBind
ATACSeq
updated 7 months ago by
James W. MacDonald
64k • written 8 months ago by
Chris
• 0
8
votes
13
replies
1.8k
views
Help with Error in DiffBind
DiffBind
ATACSeq
8 months ago
Chris
• 0
1
vote
1
reply
679
views
DiffBind on ATAC seq data
ATACSeq
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
Chris
• 0
0
votes
1
reply
429
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 9 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Hadar
• 0
0
votes
1
reply
403
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 10 months ago by
Ou, Jianhong
★ 1.3k • written 10 months ago by
tahir.msajid
• 0
0
votes
0
replies
373
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq
ATACseq
sample-size
12 months ago
gogniu
• 0
0
votes
2
replies
779
views
long computing time for TSS enrichment score
ATACSeq
updated 3 months ago by
Noah
• 0 • written 15 months ago by
Taeim
• 0
0
votes
0
replies
545
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
16 months ago
Sebastian Lewandowski
• 0
0
votes
1
reply
998
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 17 months ago by
Rory Stark
★ 5.1k • written 17 months ago by
young
• 0
2
votes
3
replies
787
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
19 months ago • updated 18 months ago
bers.anthrope
• 0
1
vote
2
replies
1.2k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
19 months ago
zgraytho88
• 0
0
votes
0
replies
443
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
20 months ago
hyjforesight
• 0
2
votes
5
replies
3.7k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 15 months ago by
eric.kern13
▴ 20 • written 2.2 years ago by
changxu.fan
▴ 20
0
votes
3
replies
930
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
updated 15 months ago by
Rory Stark
★ 5.1k • written 2.2 years ago by
adR
▴ 30
1
vote
3
replies
1.2k
views
Using block and design together in Diffbind 3.0?
DiffBind
R
ATACSeq
updated 2.4 years ago by
sbcn
▴ 80 • written 2.4 years ago by
fleur_p90
• 0
5
votes
8
replies
1.8k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 17 months ago by
Johanna Hardin
▴ 20 • written 2.4 years ago by
pegah.taklifi
▴ 30
1
vote
4
replies
1.3k
views
Binding matrix created by DiffBind
ATACSeq
DiffBind
2.5 years ago • updated 2.4 years ago
sh.kazempour94
▴ 10
2
votes
5
replies
2.7k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 11 months ago by
Junsik
• 0 • written 2.5 years ago by
Rory Stark
★ 5.1k
0
votes
4
replies
1.1k
views
DiffBind
ATACSeq
DiFFBind
2.6 years ago • updated 2.5 years ago
Riba Michela
▴ 90
1
vote
5
replies
1.5k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind
ATACSeq
updated 2.7 years ago by
James W. MacDonald
64k • written 2.7 years ago by
fleur_p90
• 0
2
votes
4
replies
1.3k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
updated 2.8 years ago by
Rory Stark
★ 5.1k • written 2.8 years ago by
Asma
• 0
1
vote
1
reply
1.4k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 3.1 years ago by
Rory Stark
★ 5.1k
1
vote
10
replies
1.8k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 3.1 years ago by
Rory Stark
★ 5.1k • written 3.1 years ago by
CodeAway
▴ 70
0
votes
4
replies
1.7k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 3.3 years ago by
Ou, Jianhong
★ 1.3k • written 3.3 years ago by
achaillon
• 0
1
vote
2
replies
7.8k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.3 years ago by
Ou, Jianhong
★ 1.3k • written 3.3 years ago by
Arpi Beshlikyan
• 0
0
votes
7
replies
1.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 4.4 years ago by
Steve Lianoglou
13k • written 4.4 years ago by
mbasam
• 0
0
votes
2
replies
1.0k
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
4.6 years ago
tangming2005
▴ 190
2
votes
1
reply
1.1k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 4.7 years ago by
Rory Stark
★ 5.1k • written 4.7 years ago by
pgontarz
▴ 10
1
vote
2
replies
1.8k
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 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
kaiser.karim
• 0
2
votes
4
replies
1.3k
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 5.2 years ago by
Rory Stark
★ 5.1k • written 5.2 years ago by
gtechbio
▴ 10
0
votes
2
replies
1.0k
views
mogsa on RNA-seq and ATAC-seq data
mogsa
atacseq
updated 5.5 years ago by
mengchen18
• 0 • written 5.5 years ago by
meeta.mistry
▴ 30
36 results • Page
1 of 1
Recent ...
Replies
Answer: Obtaining rsIDs with ENSG and variant ID information
by
Robert Castelo
★ 3.0k
You should first and foremost find out what was the human reference genome version from which your dataset was derived. Assuming this was G…
Comment: DESeq2 - groups with biological replicates from the same patient
by
James W. MacDonald
64k
If by clustering you mean there might be a within-subject correlation, then yes it's a possibility. But you cannot control for that using a…
Comment: Why is DMRcate not available for Bioconductor version 3.18?
by
Mike Smith
★ 6.2k
If we hover over the tiny little red icon next to the Linux build report, we can see that the source package isn't being distributed becaus…
Comment: ClusterProfiler - enrichKEGG on specific pathways
by
EvaLan
• 0
Hey bekah, I wonder if you have found the solution to solve this issue? Best wishes, EvaLan
Comment: Why is DMRcate not available for Bioconductor version 3.18?
by
Gordon Smyth
48k
That's a good question. On the DMRcate landing page, one can see that the "Source package" file is missing, meaning that installation in Un…
Votes
Comment: limma::voom vs edgeR::voomLmFit - when to use?
Answer: limma::voom vs edgeR::voomLmFit - when to use?
Answer: trying to add SingleR label to Seurat Object fails
Comment: DESeq2 - groups with biological replicates from the same patient
Answer: EdgeR: Exact test and glmQLFTest produce very different results
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Assa Yeroslaviz
★ 1.5k
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Gordon Smyth
48k
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▴ 70
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