Showing : atacseq • reset
0
votes
4
replies
2.0k
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
24 days ago • updated 13 days ago Mengjun • 0
0
votes
0
replies
94
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
29 days ago • updated 24 days ago info ▴ 10
0
votes
1
reply
679
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 5 months ago by ★ 4.8k • written 6 months ago by • 0
0
votes
0
replies
256
views
diffbind covariates
DiffBind ATACSeq
updated 6 months ago by 43k • written 6 months ago by ▴ 220
2
votes
5
replies
903
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
7 months ago ronin • 0
0
votes
0
replies
722
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
11 months ago Raghad • 0
0
votes
4
replies
702
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
12 months ago lonn • 0
0
votes
0
replies
458
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
13 months ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
790
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
15 months ago isaromero8888 • 0
0
votes
0
replies
794
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
15 months ago Jawahar • 0
0
votes
0
replies
547
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
16 months ago inna.gur • 0
0
votes
7
replies
1.4k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 14 months ago by ▴ 10 • written 17 months ago by • 0
0
votes
0
replies
772
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
replies
1.7k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 21 months ago by ★ 1.6k • written 21 months ago by • 0
4
votes
6
replies
1.4k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.0 years ago Chris ▴ 20
5
votes
8
replies
1.6k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.1 years ago by ▴ 20
3
votes
5
replies
1.3k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.0 years ago by 68k • written 2.1 years ago by ▴ 20
8
votes
13
replies
4.8k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.1 years ago Chris ▴ 20
2
votes
1
reply
3.8k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by ▴ 20
0
votes
1
reply
991
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
0
votes
1
reply
865
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by • 0
0
votes
0
replies
954
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
1.9k
views
long computing time for TSS enrichment score
ATACSeq
updated 20 months ago by • 0 • written 2.7 years ago by • 0
0
votes
0
replies
982
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.8 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 2.9 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 17 months ago by • 0 • written 3.0 years ago by • 0
0
votes
0
replies
857
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.1 years ago hyjforesight • 0
2
votes
5
replies
6.4k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.7 years ago by ▴ 20 • written 3.6 years ago by ▴ 20
0
votes
3
replies
1.5k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.7 years ago by ★ 5.2k • written 3.6 years ago by ▴ 40
1
vote
3
replies
2.2k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.8 years ago by ▴ 80 • written 3.8 years ago by • 0
5
votes
8
replies
3.0k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.9 years ago by ▴ 20 • written 3.8 years ago by ▴ 30
1
vote
4
replies
2.0k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.9 years ago sh.kazempour94 ▴ 10
2
votes
5
replies
5.1k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.4 years ago by • 0 • written 3.9 years ago by ★ 5.2k
0
votes
4
replies
1.9k
views
DiffBind
ATACSeq DiFFBind
4.0 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 4.1 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 4.2 years ago by ★ 5.2k • written 4.2 years ago by • 0
1
vote
1
reply
2.0k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.5 years ago by ★ 5.2k
1
vote
10
replies
3.5k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.5 years ago by ★ 5.2k • written 4.5 years ago by ▴ 70
0
votes
4
replies
2.6k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by • 0
1
vote
2
replies
13k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.7 years ago by ★ 1.3k • written 4.7 years ago by • 0
0
votes
7
replies
2.3k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.9 years ago by ★ 13k • written 5.9 years ago by • 0
0
votes
2
replies
1.6k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.0 years ago tangming2005 ▴ 200
2
votes
1
reply
1.8k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.1 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
1
vote
2
replies
2.4k
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 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
4
replies
1.8k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.6k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 30
47 results • Page 1 of 1
Recent ...
Replies
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
Awards • All
Popular Question to Shaimaa Gamal • 0
Great Question to inzirio ▴ 10
Popular Question to enee ▴ 10
Popular Question to Sam ▴ 10
Popular Question to s.malik • 0
Locations • All
The city by the bay, 3 minutes ago
WEHI, Melbourne, Australia, 16 minutes ago
United States, 1 hour ago
Türkiye, 1 hour ago
Pittsburgh, United States, 2 hours ago
Traffic: 552 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