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ATACSeq
•
reset
0
votes
0
replies
22
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
1 day ago
Hadar
• 0
0
votes
1
reply
56
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 23 days ago by
Ou, Jianhong
★ 1.3k • written 23 days ago by
tahir.msajid
• 0
0
votes
0
replies
88
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq
ATACseq
sample-size
10 weeks ago
gogniu
• 0
0
votes
0
replies
190
views
long computing time for TSS enrichment score
ATACSeq
5 months ago
Taeim
• 0
0
votes
0
replies
230
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
6 months ago
Sebastian Lewandowski
• 0
0
votes
1
reply
336
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 7 months ago by
Rory Stark
★ 4.6k • written 7 months ago by
young
• 0
2
votes
3
replies
388
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
9 months ago • updated 8 months ago
bers.anthrope
• 0
1
vote
2
replies
584
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
9 months ago
zgraytho88
• 0
0
votes
0
replies
199
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
10 months ago
hyjforesight
• 0
2
votes
5
replies
2.0k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 5 months ago by
eric.kern13
▴ 20 • written 16 months ago by
changxu.fan
▴ 10
0
votes
3
replies
478
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
updated 5 months ago by
Rory Stark
★ 4.6k • written 16 months ago by
adR
▴ 20
1
vote
3
replies
697
views
Using block and design together in Diffbind 3.0?
DiffBind
R
ATACSeq
updated 18 months ago by
sbcn
▴ 80 • written 18 months ago by
fleur_p90
• 0
5
votes
8
replies
1.1k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 7 months ago by
Johanna Hardin
▴ 20 • written 18 months ago by
pegah.taklifi
▴ 30
1
vote
4
replies
820
views
Binding matrix created by DiffBind
ATACSeq
DiffBind
19 months ago
sh.kazempour94
▴ 10
2
votes
5
replies
1.4k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 7 weeks ago by
Junsik
• 0 • written 20 months ago by
Rory Stark
★ 4.6k
0
votes
4
replies
712
views
DiffBind
ATACSeq
DiFFBind
21 months ago • updated 20 months ago
Riba Michela
▴ 90
1
vote
5
replies
1.0k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind
ATACSeq
updated 22 months ago by
James W. MacDonald
62k • written 22 months ago by
fleur_p90
• 0
2
votes
4
replies
804
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
updated 23 months ago by
Rory Stark
★ 4.6k • written 23 months ago by
Asma
• 0
1
vote
1
reply
1.0k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 2.3 years ago by
Rory Stark
★ 4.6k
1
vote
10
replies
1.1k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 2.2 years ago by
Rory Stark
★ 4.6k • written 2.3 years ago by
CodeAway
▴ 70
0
votes
4
replies
1.2k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 2.4 years ago by
Ou, Jianhong
★ 1.3k • written 2.5 years ago by
achaillon
• 0
1
vote
2
replies
5.0k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 2.5 years ago by
Ou, Jianhong
★ 1.3k • written 2.5 years ago by
Arpi Beshlikyan
• 0
0
votes
7
replies
1.1k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 3.6 years ago by
Steve Lianoglou
13k • written 3.6 years ago by
mbasam
• 0
0
votes
2
replies
668
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
3.7 years ago
tangming2005
▴ 190
2
votes
1
reply
754
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 3.9 years ago by
Rory Stark
★ 4.6k • written 3.9 years ago by
pgontarz
▴ 10
1
vote
2
replies
1.4k
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 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
kaiser.karim
• 0
2
votes
4
replies
970
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 4.3 years ago by
Rory Stark
★ 4.6k • written 4.4 years ago by
gtechbio
▴ 10
0
votes
2
replies
677
views
mogsa on RNA-seq and ATAC-seq data
mogsa
atacseq
updated 4.6 years ago by
mengchen18
• 0 • written 4.6 years ago by
meeta.mistry
▴ 30
28 results • Page
1 of 1
Recent ...
Replies
Answer: Different summary() and results() values in DeSeq2
by
swbarnes2
★ 1.2k
211k genes? That's a lot. It looks like the difference is in the gene filtering. The top one is filtering way genes with a mean counts <…
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Guido Hooiveld
★ 3.5k
Also: you could consider using `DABG` for present/absent calls. James elaborated on this in this thread: https://support.bioconductor.org/p…
Comment: mas5calls function doesn't work; mirna40cdf problem
by
James W. MacDonald
62k
Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.
Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage
by
ayabalbaa1990
• 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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