Showing : ATACseq • reset
0
votes
4
replies
2.3k
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
6 months ago Mengjun • 0
0
votes
0
replies
311
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
6 months ago info ▴ 10
0
votes
1
reply
896
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
0
replies
353
views
diffbind covariates
DiffBind ATACSeq
updated 12 months ago by 43k • written 12 months ago by ▴ 220
2
votes
5
replies
1.1k
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
13 months ago ronin • 0
0
votes
0
replies
882
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
17 months ago Raghad • 0
0
votes
4
replies
919
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
18 months ago lonn • 0
0
votes
0
replies
581
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
19 months ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
970
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
21 months ago isaromero8888 • 0
0
votes
0
replies
915
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
21 months ago Jawahar • 0
0
votes
0
replies
653
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
22 months ago inna.gur • 0
0
votes
7
replies
1.7k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 20 months ago by ▴ 10 • written 23 months ago by • 0
0
votes
0
replies
937
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
2
replies
1.9k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.2 years ago by ★ 1.6k • written 2.2 years ago by • 0
4
votes
6
replies
1.7k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.5 years ago Chris ▴ 20
5
votes
8
replies
1.8k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.6 years ago by ▴ 20
3
votes
5
replies
1.5k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.5 years ago by 68k • written 2.6 years ago by ▴ 20
8
votes
13
replies
5.3k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.6 years ago Chris ▴ 20
2
votes
1
reply
4.2k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by ▴ 20
0
votes
1
reply
1.1k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
votes
1
reply
1.0k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.8 years ago by ★ 1.3k • written 2.8 years ago by • 0
0
votes
0
replies
1.1k
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.9 years ago gogniu • 0
0
votes
2
replies
2.0k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.2 years ago by • 0 • written 3.2 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.3 years ago Sebastian Lewandowski • 0
0
votes
1
reply
2.1k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.3 years ago by ★ 5.2k • written 3.3 years ago by • 0
2
votes
3
replies
1.5k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.5 years ago • updated 3.4 years ago bers.anthrope ▴ 10
1
vote
3
replies
2.3k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 23 months ago by • 0 • written 3.5 years ago by • 0
0
votes
0
replies
957
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.6 years ago hyjforesight • 0
2
votes
5
replies
6.8k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.2 years ago by ▴ 20 • written 4.0 years ago by ▴ 20
0
votes
3
replies
1.7k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.2 years ago by ★ 5.2k • written 4.0 years ago by ▴ 40
1
vote
3
replies
2.4k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.3 years ago by ▴ 80 • written 4.3 years ago by • 0
5
votes
8
replies
3.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.4 years ago by ▴ 20 • written 4.3 years ago by ▴ 30
1
vote
4
replies
2.2k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.4 years ago • updated 4.3 years ago sh.kazempour94 ▴ 10
2
votes
5
replies
5.5k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.9 years ago by • 0 • written 4.4 years ago by ★ 5.2k
0
votes
4
replies
2.0k
views
DiffBind
ATACSeq DiFFBind
4.5 years ago • updated 4.4 years ago Riba Michela ▴ 90
1
vote
5
replies
2.6k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
2
votes
4
replies
2.2k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.6 years ago by ★ 5.2k • written 4.7 years ago by • 0
1
vote
1
reply
2.2k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.0 years ago by ★ 5.2k
1
vote
10
replies
3.9k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.9 years ago by ★ 5.2k • written 5.0 years ago by ▴ 70
0
votes
4
replies
2.8k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.2 years ago by ★ 1.3k • written 5.2 years ago by • 0
1
vote
2
replies
13k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.2 years ago by ★ 1.3k • written 5.2 years ago by • 0
0
votes
7
replies
2.5k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.3 years ago by ★ 13k • written 6.3 years ago by • 0
0
votes
2
replies
1.7k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.5 years ago tangming2005 ▴ 200
2
votes
1
reply
1.9k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by ▴ 10
1
vote
2
replies
2.5k
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 6.6 years ago by 43k • written 6.6 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 7.1 years ago by ★ 5.2k • written 7.1 years ago by ▴ 10
0
votes
2
replies
1.8k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 7.4 years ago by • 0 • written 7.4 years ago by ▴ 30
47 results • Page 1 of 1
Recent ...
Replies
Answer: Issue with Soft-Thresholding in WGCNA by misty.chickadee.vckc • 0
Hi Maria, your detailed explanation is super helpful! The NA power estimate in WGCNA can be tricky. I've sometimes seen that when the data …
Comment: Interpretation of output of AffyRNAdeg and hist commands by debasainalsa • 0
When working with AffyRNAdeg output it helps to think of the table like browsing a HEYTEA Menu each row shows a feature of your slides and …
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to jf1 • 0
Popular Question to dan.gatti • 0
Popular Question to shepherl 4.2k
Locations • All
WEHI, Melbourne, Australia, 4 minutes ago
The city by the bay, 27 minutes ago
Japan, 1 hour ago
United States, 2 hours ago
United States, 3 hours ago
Traffic: 989 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