Showing : ATACseq • reset
0
votes
1
reply
243
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
updated 1 day ago by ★ 4.8k • written 1 day ago by • 0
0
votes
0
replies
38
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
5 days ago • updated 1 day ago info ▴ 10
0
votes
1
reply
623
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 5 months ago by ★ 4.8k • written 5 months ago by • 0
0
votes
0
replies
232
views
diffbind covariates
DiffBind ATACSeq
updated 5 months ago by 43k • written 5 months ago by ▴ 220
2
votes
5
replies
870
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
6 months ago ronin • 0
0
votes
0
replies
667
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
10 months ago Raghad • 0
0
votes
4
replies
679
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
11 months ago lonn • 0
0
votes
0
replies
436
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
12 months ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
765
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
14 months ago isaromero8888 • 0
0
votes
0
replies
762
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
14 months ago Jawahar • 0
0
votes
0
replies
523
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
15 months ago inna.gur • 0
0
votes
7
replies
1.4k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 13 months ago by ▴ 10 • written 16 months ago by • 0
0
votes
0
replies
747
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
2
replies
1.7k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 20 months ago by ★ 1.6k • written 20 months ago by • 0
4
votes
6
replies
1.4k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
24 months ago • updated 23 months ago Chris ▴ 20
5
votes
8
replies
1.6k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.0 years ago by ▴ 20
3
votes
5
replies
1.3k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 23 months ago by 68k • written 2.0 years ago by ▴ 20
8
votes
13
replies
4.6k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.0 years ago Chris ▴ 20
2
votes
1
reply
3.7k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.0 years ago by ★ 5.2k • written 2.0 years ago by ▴ 20
0
votes
1
reply
960
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.1 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
1
reply
844
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.2 years ago by ★ 1.3k • written 2.2 years ago by • 0
0
votes
0
replies
928
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.4 years ago gogniu • 0
0
votes
2
replies
1.8k
views
long computing time for TSS enrichment score
ATACSeq
updated 19 months ago by • 0 • written 2.6 years ago by • 0
0
votes
0
replies
966
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.7 years ago Sebastian Lewandowski • 0
0
votes
1
reply
1.9k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.8 years ago by ★ 5.2k • written 2.8 years ago by • 0
2
votes
3
replies
1.3k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.0 years ago • updated 2.9 years ago bers.anthrope ▴ 10
1
vote
3
replies
2.1k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 16 months ago by • 0 • written 2.9 years ago by • 0
0
votes
0
replies
837
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.1 years ago hyjforesight • 0
2
votes
5
replies
6.2k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.6 years ago by ▴ 20 • written 3.5 years ago by ▴ 20
0
votes
3
replies
1.5k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.6 years ago by ★ 5.2k • written 3.5 years ago by ▴ 40
1
vote
3
replies
2.1k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.7 years ago by ▴ 80 • written 3.7 years ago by • 0
5
votes
8
replies
2.9k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.8 years ago by ▴ 20 • written 3.7 years ago by ▴ 30
1
vote
4
replies
2.0k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.8 years ago sh.kazempour94 ▴ 10
2
votes
5
replies
5.0k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.3 years ago by • 0 • written 3.9 years ago by ★ 5.2k
0
votes
4
replies
1.8k
views
DiffBind
ATACSeq DiFFBind
4.0 years ago • updated 3.9 years ago Riba Michela ▴ 90
1
vote
5
replies
2.3k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4.0 years ago by 68k • written 4.1 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by • 0
1
vote
1
reply
2.0k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.4 years ago by ★ 5.2k
1
vote
10
replies
3.4k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.4 years ago by ★ 5.2k • written 4.5 years ago by ▴ 70
0
votes
4
replies
2.5k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by • 0
1
vote
2
replies
12k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.6 years ago by ★ 1.3k • written 4.7 years ago by • 0
0
votes
7
replies
2.2k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.8 years ago by ★ 13k • written 5.8 years ago by • 0
0
votes
2
replies
1.5k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.9 years ago tangming2005 ▴ 200
2
votes
1
reply
1.7k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
1
vote
2
replies
2.3k
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 6.1 years ago by 43k • written 6.1 years ago by • 0
2
votes
4
replies
1.8k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.5 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.8 years ago by • 0 • written 6.8 years ago by ▴ 30
47 results • Page 1 of 1
Recent ...
Replies
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.8k
That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
Awards • All
Popular Question to pcantalupo ▴ 10
Popular Question to bioinformaticssrm2011 • 0
Popular Question to slizchap • 0
Scholar to Aaron Lun ★ 28k
Scholar to James W. MacDonald 68k
Locations • All
Canada, 4 minutes ago
United Kingdom, 26 minutes ago
United States, 38 minutes ago
Switzerland, 52 minutes ago
United Kingdom, 1 hour ago
Traffic: 637 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6