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atacseq
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Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
18 days ago
Sebastian Lewandowski
• 0
0
votes
1
reply
122
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 5 weeks ago by
Rory Stark
★ 4.4k • written 7 weeks ago by
young
• 0
2
votes
3
replies
232
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
3 months ago • updated 10 weeks ago
bers.anthrope
• 0
1
vote
2
replies
295
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
3 months ago
zgraytho88
• 0
0
votes
0
replies
105
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
4 months ago
hyjforesight
• 0
2
votes
4
replies
1.3k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 10 months ago by
Michael Love
37k • written 10 months ago by
changxu.fan
▴ 10
0
votes
2
replies
297
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
10 months ago
adR
▴ 10
1
vote
3
replies
471
views
Using block and design together in Diffbind 3.0?
DiffBind
R
ATACSeq
updated 12 months ago by
sbcn
▴ 80 • written 12 months ago by
fleur_p90
• 0
5
votes
8
replies
841
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 8 weeks ago by
Johanna Hardin
▴ 20 • written 13 months ago by
pegah.taklifi
▴ 30
1
vote
4
replies
616
views
Binding matrix created by DiffBind
ATACSeq
DiffBind
14 months ago • updated 13 months ago
sh.kazempour94
▴ 10
1
vote
2
replies
886
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
14 months ago • updated 11 months ago
Rory Stark
★ 4.4k
0
votes
4
replies
547
views
DiffBind
ATACSeq
DiFFBind
15 months ago • updated 14 months ago
Riba Michela
▴ 90
1
vote
5
replies
754
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind
ATACSeq
updated 16 months ago by
James W. MacDonald
60k • written 17 months ago by
fleur_p90
• 0
2
votes
4
replies
575
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
updated 17 months ago by
Rory Stark
★ 4.4k • written 17 months ago by
Asma
• 0
1
vote
1
reply
883
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 21 months ago by
Rory Stark
★ 4.4k
1
vote
10
replies
835
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 21 months ago by
Rory Stark
★ 4.4k • written 21 months ago by
CodeAway
▴ 70
0
votes
4
replies
926
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 23 months ago by
Ou, Jianhong
★ 1.3k • written 23 months ago by
achaillon
• 0
1
vote
2
replies
3.5k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 24 months ago by
Ou, Jianhong
★ 1.3k • written 2.0 years ago by
Arpi Beshlikyan
• 0
0
votes
7
replies
920
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 3.1 years ago by
Steve Lianoglou
13k • written 3.1 years ago by
mbasam
• 0
0
votes
2
replies
537
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
3.3 years ago
tangming2005
▴ 190
2
votes
1
reply
635
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 3.4 years ago by
Rory Stark
★ 4.4k • written 3.4 years ago by
pgontarz
▴ 10
1
vote
2
replies
1.3k
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 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
kaiser.karim
• 0
2
votes
4
replies
865
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 3.9 years ago by
Rory Stark
★ 4.4k • written 3.9 years ago by
gtechbio
▴ 10
0
votes
2
replies
574
views
mogsa on RNA-seq and ATAC-seq data
mogsa
atacseq
updated 4.1 years ago by
mengchen18
• 0 • written 4.2 years ago by
meeta.mistry
▴ 30
24 results • Page
1 of 1
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Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Comment: unable to install.packages("spatialLIBD")
by
Leonardo Collado Torres
▴ 1000
All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…
Answer: how to use Rsamtools to parse extra fields from STAR alignment
by
Martin Morgan
25k
The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Delta._.43
▴ 10
Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
by
Alejandro Reyes
★ 1.8k
Thanks for your detail post. I think this might be related to this issue here: https://support.bioconductor.org/p/9143537/ Just to verify…
Votes
Answer: spot- vs cell-level data access
Answer: unable to install.packages("spatialLIBD")
Comment: unable to install.packages("spatialLIBD")
error running UniProt.ws
Answer: DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FU
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▴ 1000
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