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ATACSeq
•
reset
0
votes
2
replies
249
views
ATACseq rudimentary questions
ATACSeq
DiffBind
8 weeks ago • updated 7 weeks ago
4747
• 0
0
votes
4
replies
2.5k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
10 months ago
Mengjun
• 0
0
votes
0
replies
431
views
News:
Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq
MNaseSeq
ATACSeq
11 months ago • updated 10 months ago
info
▴ 10
0
votes
1
reply
1.1k
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 16 months ago by
ATpoint
★ 5.0k • written 16 months ago by
Katerina
• 0
0
votes
0
replies
494
views
diffbind covariates
DiffBind
ATACSeq
updated 16 months ago by
Michael Love
43k • written 16 months ago by
Alpesh Querer
▴ 220
2
votes
5
replies
1.3k
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes
ATACSeq
17 months ago
ronin
• 0
0
votes
0
replies
1.2k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
21 months ago
Raghad
• 0
0
votes
4
replies
1.0k
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
22 months ago
lonn
• 0
0
votes
0
replies
725
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
23 months ago
Pierre Lindenbaum
▴ 10
0
votes
1
reply
1.2k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
2.1 years ago
isaromero8888
• 0
0
votes
0
replies
1.1k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
2.1 years ago
Jawahar
• 0
0
votes
0
replies
750
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
2.2 years ago
inna.gur
• 0
0
votes
7
replies
1.9k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 24 months ago by
danalvoronov
▴ 10 • written 2.2 years ago by
jfmay
• 0
0
votes
0
replies
1.0k
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
sophie.hfliu
• 0
0
votes
2
replies
2.3k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 2.6 years ago by
Malcolm Cook
★ 1.6k • written 2.6 years ago by
Nebat
• 0
4
votes
6
replies
1.8k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
2.9 years ago
Chris
▴ 20
5
votes
8
replies
2.0k
views
Help with error install csaw
ChIPSeq
ATACSeq
written 2.9 years ago by
Chris
▴ 20
3
votes
5
replies
1.7k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
Chris
▴ 20
8
votes
13
replies
5.8k
views
Help with Error in DiffBind
DiffBind
ATACSeq
2.9 years ago
Chris
▴ 20
2
votes
1
reply
4.8k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.9 years ago by
Rory Stark
★ 5.3k • written 2.9 years ago by
Chris
▴ 20
0
votes
1
reply
1.3k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 3.0 years ago by
Rory Stark
★ 5.3k • written 3.1 years ago by
Hadar
• 0
0
votes
1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 3.1 years ago by
Ou, Jianhong
★ 1.4k • written 3.1 years ago by
tahir.msajid
• 0
0
votes
0
replies
1.2k
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq
ATACseq
sample-size
3.3 years ago
gogniu
• 0
0
votes
2
replies
2.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.5 years ago by
Noah
• 0 • written 3.5 years ago by
Taeim
• 0
0
votes
0
replies
1.2k
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
3.6 years ago
Sebastian Lewandowski
• 0
0
votes
1
reply
2.4k
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 3.6 years ago by
Rory Stark
★ 5.3k • written 3.7 years ago by
young
• 0
2
votes
3
replies
1.8k
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
3.9 years ago • updated 3.8 years ago
bers.anthrope
▴ 10
1
vote
3
replies
2.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 2.2 years ago by
dineika.chandrananda
• 0 • written 3.8 years ago by
zgraytho88
• 0
0
votes
0
replies
1.1k
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
4.0 years ago
hyjforesight
• 0
2
votes
5
replies
7.3k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 3.5 years ago by
eric.kern13
▴ 20 • written 4.4 years ago by
changxu.fan
▴ 20
0
votes
3
replies
1.9k
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
updated 3.5 years ago by
Rory Stark
★ 5.3k • written 4.4 years ago by
adR
▴ 40
1
vote
3
replies
2.6k
views
Using block and design together in Diffbind 3.0?
DiffBind
R
ATACSeq
updated 4.6 years ago by
sbcn
▴ 80 • written 4.6 years ago by
fleur_p90
• 0
5
votes
8
replies
3.5k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 3.7 years ago by
Johanna Hardin
▴ 20 • written 4.6 years ago by
pegah.taklifi
▴ 30
1
vote
4
replies
2.4k
views
Binding matrix created by DiffBind
ATACSeq
DiffBind
4.7 years ago
sh.kazempour94
▴ 10
2
votes
5
replies
6.0k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 3.2 years ago by
Junsik
• 0 • written 4.8 years ago by
Rory Stark
★ 5.3k
0
votes
4
replies
2.2k
views
DiffBind
ATACSeq
DiFFBind
4.9 years ago • updated 4.8 years ago
Riba Michela
▴ 90
1
vote
5
replies
2.7k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind
ATACSeq
updated 4.9 years ago by
James W. MacDonald
68k • written 4.9 years ago by
fleur_p90
• 0
2
votes
4
replies
2.4k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
updated 5.0 years ago by
Rory Stark
★ 5.3k • written 5.0 years ago by
Asma
• 0
1
vote
1
reply
2.4k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 5.3 years ago by
Rory Stark
★ 5.3k
1
vote
10
replies
4.3k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 5.3 years ago by
Rory Stark
★ 5.3k • written 5.4 years ago by
CodeAway
▴ 70
0
votes
4
replies
3.4k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 5.5 years ago by
Ou, Jianhong
★ 1.4k • written 5.5 years ago by
achaillon
• 0
1
vote
2
replies
15k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 5.5 years ago by
Ou, Jianhong
★ 1.4k • written 5.6 years ago by
Arpi Beshlikyan
• 0
0
votes
7
replies
2.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 6.7 years ago by
Steve Lianoglou
★ 13k • written 6.7 years ago by
mbasam
• 0
0
votes
2
replies
1.9k
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
6.8 years ago
tangming2005
▴ 200
2
votes
1
reply
2.1k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 6.9 years ago by
Rory Stark
★ 5.3k • written 7.0 years ago by
pgontarz
▴ 10
1
vote
2
replies
2.7k
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 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
kaiser.karim
• 0
2
votes
4
replies
2.1k
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 7.4 years ago by
Rory Stark
★ 5.3k • written 7.4 years ago by
gtechbio
▴ 10
0
votes
2
replies
2.0k
views
mogsa on RNA-seq and ATAC-seq data
mogsa
atacseq
updated 7.7 years ago by
mengchen18
• 0 • written 7.7 years ago by
meeta.mistry
▴ 30
48 results • Page
1 of 1
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Comment: Can sample-level weights be used when analysing GSVA scores in limma?
by
A.Barden
▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions
by
Gordon Smyth
53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack
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Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
strawberry3
• 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
by
James W. MacDonald
68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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