Showing : ATACseq • reset
8
votes
13
replies
4.2k
views
Help with Error in DiffBind
DiffBind ATACSeq
22 months ago • updated 21 months ago Chris ▴ 20
1
vote
10
replies
3.1k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.2 years ago by ★ 5.2k • written 4.2 years ago by ▴ 70
5
votes
8
replies
2.7k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.6 years ago by ▴ 20 • written 3.5 years ago by ▴ 30
5
votes
8
replies
1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
0
votes
7
replies
1.2k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 10 months ago by ▴ 10 • written 13 months ago by • 0
0
votes
7
replies
2.1k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.6 years ago by ★ 13k • written 5.6 years ago by • 0
4
votes
6
replies
1.3k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
21 months ago Chris ▴ 20
3
votes
5
replies
1.2k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 21 months ago by 67k • written 21 months ago by ▴ 20
2
votes
5
replies
737
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
4 months ago ronin • 0
2
votes
5
replies
5.7k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.4 years ago by ▴ 20 • written 3.3 years ago by ▴ 20
1
vote
5
replies
2.2k
views
How to add chr to an dba object before differential analysis to enable removing blacklisted regions
DiffBind ATACSeq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
2
votes
5
replies
4.6k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.1 years ago by • 0 • written 3.7 years ago by ★ 5.2k
0
votes
4
replies
1.7k
views
DiffBind
ATACSeq DiFFBind
3.7 years ago Riba Michela ▴ 90
2
votes
4
replies
1.7k
views
DiffBind confuses coordinates of peaks
atacseq diffbind
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
0
votes
4
replies
2.4k
views
ATACseqQC R package for QC scores (TSS, FRIP, NFR, IDR)
ATACseqQC atacseq R
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
0
votes
4
replies
586
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
9 months ago lonn • 0
2
votes
4
replies
1.9k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 3.9 years ago by ★ 5.2k • written 3.9 years ago by • 0
1
vote
4
replies
1.9k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.6 years ago sh.kazempour94 ▴ 10
1
vote
3
replies
2.0k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq regionCounts csaw
updated 13 months ago by • 0 • written 2.7 years ago by • 0
2
votes
3
replies
1.2k
views
DiffBind always reverts to default normalization
ATACSeq Normalization DiffBind
2.7 years ago bers.anthrope ▴ 10
1
vote
3
replies
2.0k
views
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.5 years ago by ▴ 80 • written 3.5 years ago by • 0
0
votes
3
replies
1.4k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.4 years ago by ★ 5.2k • written 3.3 years ago by ▴ 40
0
votes
2
replies
1.5k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 18 months ago by ★ 1.6k • written 18 months ago by • 0
1
vote
2
replies
12k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
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 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
2
replies
1.7k
views
long computing time for TSS enrichment score
ATACSeq
updated 17 months ago by • 0 • written 2.4 years ago by • 0
0
votes
2
replies
1.4k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 30
0
votes
2
replies
1.5k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.7 years ago tangming2005 ▴ 200
0
votes
1
reply
795
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
0
votes
1
reply
397
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
2
votes
1
reply
3.1k
views
DiffBind on ATAC seq data
ATACSeq
updated 22 months ago by ★ 5.2k • written 22 months ago by ▴ 20
1
vote
1
reply
1.9k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.2 years ago by ★ 5.2k
2
votes
1
reply
1.6k
views
Using DiffBind with only a counts table?
diffbind ATACseq ATAC counts differential analysis
updated 5.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
votes
1
reply
887
views
DiffBind- differentiate between new peaks and gain peaks
ATAC DiffBind ATACSeq
updated 23 months ago by ★ 5.2k • written 23 months ago by • 0
0
votes
1
reply
650
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
11 months ago isaromero8888 • 0
0
votes
0
replies
912
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.5 years ago Sebastian Lewandowski • 0
0
votes
0
replies
502
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
8 months ago Raghad • 0
0
votes
0
replies
664
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 months ago Jawahar • 0
0
votes
0
replies
677
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 15 months ago by 67k • written 15 months ago by • 0
0
votes
0
replies
848
views
How we could calculate the sample size for ATAC seq and single cell RNA seq, respectively?
singlecellRNAseq ATACseq sample-size
2.2 years ago gogniu • 0
0
votes
0
replies
798
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
2.8 years ago hyjforesight • 0
0
votes
0
replies
365
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
9 months ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
155
views
diffbind covariates
DiffBind ATACSeq
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 220
0
votes
0
replies
473
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
12 months ago inna.gur • 0
45 results • Page 1 of 1
Recent ...
Replies
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to Bob ▴ 10
Popular Question to shepherl 4.1k
Scholar to James W. MacDonald 67k
Popular Question to Assa Yeroslaviz ★ 1.5k
Locations • All
UPF, Barcelona, Spain, 44 minutes ago
United States, 1 hour ago
Italy, 2 hours ago
Kazakhstan, 3 hours ago
San Diego, 4 hours ago
Traffic: 651 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