Showing : ATACSeq • reset
0
votes
1
reply
589
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
0
votes
0
replies
222
views
diffbind covariates
DiffBind ATACSeq
updated 4 months ago by 43k • written 4 months ago by ▴ 220
2
votes
5
replies
843
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
627
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
10 months ago Raghad • 0
0
votes
4
replies
668
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
426
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
12 months ago Pierre Lindenbaum ▴ 10
0
votes
1
reply
754
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
741
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
518
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 12 months ago by ▴ 10 • written 16 months ago by • 0
0
votes
0
replies
737
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
2
replies
1.6k
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
23 months ago Chris ▴ 20
5
votes
8
replies
1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 24 months 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 24 months ago by ▴ 20
8
votes
13
replies
4.5k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.0 years ago • updated 24 months ago Chris ▴ 20
2
votes
1
reply
3.6k
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
944
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
0
votes
1
reply
834
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
911
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.3 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
964
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 2.7 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
2.9 years ago • updated 2.8 years ago bers.anthrope ▴ 10
1
vote
3
replies
2.1k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 15 months ago by • 0 • written 2.9 years ago by • 0
0
votes
0
replies
835
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.0 years ago hyjforesight • 0
2
votes
5
replies
6.1k
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
4.9k
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 3.8 years ago by ★ 5.2k
0
votes
4
replies
1.8k
views
DiffBind
ATACSeq DiFFBind
3.9 years ago • updated 3.8 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 4.0 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
1.9k
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
3.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.4 years ago by ★ 5.2k • written 4.4 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 4.6 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 6.0 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 6.5 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
45 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to L ▴ 50
Popular Question to boczniak767 ▴ 740
Popular Question to Luca • 0
Locations • All
Germany, 34 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Mexico, 3 hours ago
The city by the bay, 3 hours ago
Pittsburgh, United States, 6 hours ago
Traffic: 845 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