Showing : ATACseq • reset
0
votes
2
replies
177
views
ATACseq rudimentary questions
ATACSeq DiffBind
25 days ago • updated 19 days ago 4747 • 0
0
votes
4
replies
2.4k
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
9 months ago Mengjun • 0
0
votes
0
replies
396
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
9 months ago info ▴ 10
0
votes
1
reply
1.0k
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
0
replies
455
views
diffbind covariates
DiffBind ATACSeq
updated 15 months ago by 43k • written 15 months ago by ▴ 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
16 months ago ronin • 0
0
votes
0
replies
1.1k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
20 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
21 months ago lonn • 0
0
votes
0
replies
680
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
22 months ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
1.1k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
24 months ago isaromero8888 • 0
0
votes
0
replies
1.0k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
2.0 years ago Jawahar • 0
0
votes
0
replies
718
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
2.1 years ago inna.gur • 0
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 23 months ago by ▴ 10 • written 2.2 years ago by • 0
0
votes
0
replies
997
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
replies
2.1k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by • 0
4
votes
6
replies
1.8k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
2.8 years ago Chris ▴ 20
3
votes
5
replies
1.7k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 2.8 years ago by 68k • written 2.8 years ago by ▴ 20
5
votes
8
replies
2.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.8 years ago by ▴ 20
8
votes
13
replies
5.6k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.8 years ago Chris ▴ 20
2
votes
1
reply
4.5k
views
DiffBind on ATAC seq data
ATACSeq
updated 2.8 years ago by ★ 5.2k • written 2.8 years ago by ▴ 20
0
votes
1
reply
1.3k
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.9 years ago by ★ 5.2k • written 3.0 years ago by • 0
0
votes
1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 3.0 years ago by ★ 1.3k • written 3.0 years ago by • 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
3.2 years ago gogniu • 0
0
votes
2
replies
2.1k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.4 years ago by • 0 • written 3.4 years ago by • 0
0
votes
0
replies
1.2k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.5 years ago Sebastian Lewandowski • 0
0
votes
1
reply
2.2k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
1
vote
3
replies
2.6k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 2.1 years ago by • 0 • written 3.7 years ago by • 0
2
votes
3
replies
1.7k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
3.8 years ago • updated 3.7 years ago bers.anthrope ▴ 10
0
votes
0
replies
1.0k
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.9 years ago hyjforesight • 0
2
votes
5
replies
7.1k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.4 years ago by ▴ 20 • written 4.3 years ago by ▴ 20
0
votes
3
replies
1.8k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 3.4 years ago by ★ 5.2k • written 4.3 years ago by ▴ 40
1
vote
3
replies
2.5k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 4.5 years ago by ▴ 80 • written 4.5 years ago by • 0
5
votes
8
replies
3.4k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.6 years ago by ▴ 20 • written 4.5 years ago by ▴ 30
1
vote
4
replies
2.4k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.6 years ago sh.kazempour94 ▴ 10
2
votes
5
replies
5.8k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.1 years ago by • 0 • written 4.7 years ago by ★ 5.2k
0
votes
4
replies
2.1k
views
DiffBind
ATACSeq DiFFBind
4.8 years ago • updated 4.7 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 4.8 years ago by 68k • written 4.9 years ago by • 0
2
votes
4
replies
2.3k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
1
vote
1
reply
2.3k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.2 years ago by ★ 5.2k
1
vote
10
replies
4.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.2 years ago by ★ 5.2k • written 5.3 years ago by ▴ 70
0
votes
4
replies
3.2k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 5.4 years ago by ★ 1.3k • written 5.4 years ago by • 0
1
vote
2
replies
14k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 5.4 years ago by ★ 1.3k • written 5.5 years ago by • 0
0
votes
7
replies
2.6k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 6.6 years ago by ★ 13k • written 6.6 years ago by • 0
0
votes
2
replies
1.8k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.7 years ago tangming2005 ▴ 200
2
votes
1
reply
2.0k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 6.8 years ago by ★ 5.2k • written 6.9 years ago by ▴ 10
1
vote
2
replies
2.6k
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 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
4
replies
2.0k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by ▴ 10
0
votes
2
replies
1.9k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 7.6 years ago by • 0 • written 7.6 years ago by ▴ 30
48 results • Page 1 of 1
Recent ...
Replies
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to ATpoint ★ 5.0k
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
United States, 3 minutes ago
United States, 8 minutes ago
United States, 11 minutes ago
United States, 22 minutes ago
United States, 29 minutes ago
Traffic: 1397 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