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ATACSeq
•
reset
0
votes
1
reply
228
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
7 weeks ago
isaromero8888
• 0
0
votes
0
replies
147
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
8 weeks ago
Jawahar
• 0
0
votes
0
replies
185
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
11 weeks ago
inna.gur
• 0
0
votes
7
replies
554
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 17 days ago by
danalvoronov
▴ 10 • written 3 months ago by
jfmay
• 0
0
votes
0
replies
327
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
sophie.hfliu
• 0
0
votes
2
replies
729
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 7 months ago by
Malcolm Cook
★ 1.6k • written 7 months ago by
Nebat
• 0
4
votes
6
replies
847
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
11 months ago
Chris
• 0
5
votes
8
replies
922
views
Help with error install csaw
ChIPSeq
ATACSeq
updated 11 months ago by
nekisaf309
• 0 • written 11 months ago by
Chris
• 0
3
votes
5
replies
777
views
How to annotate genes from results of DiffBind
ATACSeq
updated 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Chris
• 0
8
votes
13
replies
2.5k
views
Help with Error in DiffBind
DiffBind
ATACSeq
12 months ago • updated 11 months ago
Chris
• 0
2
votes
1
reply
1.3k
views
DiffBind on ATAC seq data
ATACSeq
updated 12 months ago by
Rory Stark
★ 5.1k • written 12 months ago by
Chris
• 0
0
votes
1
reply
621
views
DiffBind- differentiate between new peaks and gain peaks
ATAC
DiffBind
ATACSeq
updated 13 months ago by
Rory Stark
★ 5.1k • written 13 months ago by
Hadar
• 0
0
votes
1
reply
515
views
Error in ATACseqQC bamQC analysis
ATACSeq
ATACseqQC
updated 14 months ago by
Ou, Jianhong
★ 1.3k • written 14 months ago by
tahir.msajid
• 0
0
votes
0
replies
511
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq
ATACseq
sample-size
16 months ago
gogniu
• 0
0
votes
2
replies
1.1k
views
long computing time for TSS enrichment score
ATACSeq
updated 6 months ago by
Noah
• 0 • written 18 months ago by
Taeim
• 0
0
votes
0
replies
669
views
Job:
Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq
multiOmicsViz
scRNAseq
JobPosting
20 months ago
Sebastian Lewandowski
• 0
0
votes
1
reply
1.2k
views
Diffbind analysis of ATAC-seq data
ATACSeq
DiffBind
updated 20 months ago by
Rory Stark
★ 5.1k • written 21 months ago by
young
• 0
2
votes
3
replies
899
views
DiffBind always reverts to default normalization
ATACSeq
Normalization
DiffBind
23 months ago • updated 22 months ago
bers.anthrope
• 0
1
vote
3
replies
1.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 3 months ago by
dineika.chandrananda
• 0 • written 22 months ago by
zgraytho88
• 0
0
votes
0
replies
537
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC
ATACSeq
2.0 years ago
hyjforesight
• 0
2
votes
5
replies
4.2k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 19 months ago by
eric.kern13
▴ 20 • written 2.4 years ago by
changxu.fan
▴ 20
0
votes
3
replies
1.1k
views
package for ATACseq data analysis
SequencingData
ATACSeq
ATACseqQC
updated 19 months ago by
Rory Stark
★ 5.1k • written 2.4 years ago by
adR
▴ 30
1
vote
3
replies
1.4k
views
Using block and design together in Diffbind 3.0?
DiffBind
R
ATACSeq
updated 2.7 years ago by
sbcn
▴ 80 • written 2.7 years ago by
fleur_p90
• 0
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 21 months ago by
Johanna Hardin
▴ 20 • written 2.7 years ago by
pegah.taklifi
▴ 30
1
vote
4
replies
1.4k
views
Binding matrix created by DiffBind
ATACSeq
DiffBind
2.8 years ago • updated 2.7 years ago
sh.kazempour94
▴ 10
2
votes
5
replies
3.1k
views
News:
New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr
ATACSeq
DiffBind
ComplexHeatmap
ChIPSeq
updated 15 months ago by
Junsik
• 0 • written 2.8 years ago by
Rory Stark
★ 5.1k
0
votes
4
replies
1.2k
views
DiffBind
ATACSeq
DiFFBind
2.9 years ago • updated 2.8 years ago
Riba Michela
▴ 90
1
vote
5
replies
1.6k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind
ATACSeq
updated 3.0 years ago by
James W. MacDonald
65k • written 3.0 years ago by
fleur_p90
• 0
2
votes
4
replies
1.5k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq
DiffBind
updated 3.0 years ago by
Rory Stark
★ 5.1k • written 3.1 years ago by
Asma
• 0
1
vote
1
reply
1.5k
views
News:
Extensive updates in DiffBind 3.0
Normalization
ATACSeq
ChIPSeq
DiffBind
chipseq
written 3.4 years ago by
Rory Stark
★ 5.1k
1
vote
10
replies
2.2k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 3.4 years ago by
Rory Stark
★ 5.1k • written 3.4 years ago by
CodeAway
▴ 70
0
votes
4
replies
1.9k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC
atacseq
R
updated 3.6 years ago by
Ou, Jianhong
★ 1.3k • written 3.6 years ago by
achaillon
• 0
1
vote
2
replies
8.9k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.6 years ago by
Ou, Jianhong
★ 1.3k • written 3.6 years ago by
Arpi Beshlikyan
• 0
0
votes
7
replies
1.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 4.7 years ago by
Steve Lianoglou
★ 13k • written 4.7 years ago by
mbasam
• 0
0
votes
2
replies
1.2k
views
calculating TSS enrichment from ATACseq data
GenomicRanges
Views
ATACseq
TSS
4.9 years ago
tangming2005
▴ 190
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.0 years ago by
Rory Stark
★ 5.1k • written 5.0 years ago by
pgontarz
▴ 10
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 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
kaiser.karim
• 0
2
votes
4
replies
1.4k
views
DiffBind confuses coordinates of peaks
atacseq
diffbind
updated 5.5 years ago by
Rory Stark
★ 5.1k • written 5.5 years ago by
gtechbio
▴ 10
0
votes
2
replies
1.1k
views
mogsa on RNA-seq and ATAC-seq data
mogsa
atacseq
updated 5.8 years ago by
mengchen18
• 0 • written 5.8 years ago by
meeta.mistry
▴ 30
39 results • Page
1 of 1
Recent ...
Replies
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
James W. MacDonald
65k
Let's take a closer look. ``` > library(GEOquery) ## some random data > getGEOSuppFiles("GSE193983") > setwd("GSE193983/") > untar("GSE19…
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Votes
Comment: DEG Filtering
Answer: DEG Filtering
Answer: DEG Filtering
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
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