Showing : ATACseq • reset
8
votes
13
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5.6k
views
Help with Error in DiffBind
DiffBind ATACSeq
2.8 years ago Chris ▴ 20
5
votes
8
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1.9k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.8 years ago by ▴ 20
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
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
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
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
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
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
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
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
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
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
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
1
vote
10
replies
4.0k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 5.2 years ago by ★ 5.2k • written 5.3 years ago by ▴ 70
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 4.8 years ago by • 0
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
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
1
vote
3
replies
2.5k
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
1
vote
4
replies
2.4k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
4.6 years ago sh.kazempour94 ▴ 10
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
0
votes
0
replies
452
views
diffbind covariates
DiffBind ATACSeq
updated 15 months ago by 43k • written 15 months ago by ▴ 220
0
votes
0
replies
717
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
2.1 years ago inna.gur • 0
0
votes
2
replies
175
views
ATACseq rudimentary questions
ATACSeq DiffBind
24 days ago • updated 18 days ago 4747 • 0
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
393
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
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
0
votes
4
replies
2.4k
views
DiffBind can't find a DAR
dar ATACSeq DiffBind
9 months ago Mengjun • 0
0
votes
2
replies
1.8k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
6.7 years ago tangming2005 ▴ 200
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
4
replies
3.1k
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
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
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
4
replies
2.1k
views
DiffBind
ATACSeq DiFFBind
4.8 years ago • updated 4.7 years ago Riba Michela ▴ 90
0
votes
7
replies
1.8k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 23 months ago by ▴ 10 • written 2.1 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
0
replies
1.1k
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
20 months ago Raghad • 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
1.0k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
2.0 years ago Jawahar • 0
0
votes
1
reply
2.2k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 3.5 years ago by ★ 5.2k • written 3.6 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
0
votes
0
replies
996
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
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
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
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
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.9 years ago hyjforesight • 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
679
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
22 months ago Pierre Lindenbaum ▴ 10
48 results • Page 1 of 1
Recent ...
Replies
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You may want to look at the coefficients you are trying to estimate with ExploreModelMatrix: https://www.bioconductor.org/packages/relea…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by emily.wolfrum • 0
Hi Gordon, Thanks for the quick reply. The technical or process blank samples I'm referring to are part of a set of quality control sampl…
Answer: Are individual-mouse-based statistics possible in CellChat? by ATpoint ★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups by ATpoint ★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Votes
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
Answer: When to use edgeR or limma
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