Showing : ATACseq • reset
8
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13
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4.5k
views
Help with Error in DiffBind
DiffBind ATACSeq
24 months ago • updated 23 months ago Chris ▴ 20
1
vote
10
replies
3.3k
views
DiffBind for ATACseq without replicates
DiffBind ATACseq replicate
updated 4.3 years ago by ★ 5.2k • written 4.4 years ago by ▴ 70
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
5
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8
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1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 23 months ago by ▴ 20
0
votes
7
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1.3k
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 12 months ago by ▴ 10 • written 15 months ago by • 0
0
votes
7
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2.2k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.7 years ago by ★ 13k • written 5.7 years ago by • 0
4
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6
replies
1.4k
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind ATACSeq
23 months ago Chris ▴ 20
3
votes
5
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1.3k
views
How to annotate genes from results of DiffBind
ATACSeq
updated 23 months ago by 68k • written 23 months ago by ▴ 20
2
votes
5
replies
830
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 • updated 5 months ago ronin • 0
2
votes
5
replies
6.1k
views
using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 2.6 years ago by ▴ 20 • written 3.4 years ago by ▴ 20
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
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
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
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
0
votes
4
replies
665
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
11 months ago lonn • 0
2
votes
4
replies
2.0k
views
DiffBind analysis for ATAC-Seq error Error processing one or more read files
ATACSeq DiffBind
updated 4.0 years ago by ★ 5.2k • written 4.1 years ago by • 0
1
vote
4
replies
2.0k
views
Binding matrix created by DiffBind
ATACSeq DiffBind
3.8 years ago • updated 3.7 years ago sh.kazempour94 ▴ 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
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
Using block and design together in Diffbind 3.0?
DiffBind R ATACSeq
updated 3.6 years ago by ▴ 80 • written 3.7 years ago by • 0
0
votes
3
replies
1.5k
views
package for ATACseq data analysis
SequencingData ATACSeq ATACseqQC
updated 2.6 years ago by ★ 5.2k • written 3.4 years ago by ▴ 40
0
votes
2
replies
1.6k
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 19 months ago by ★ 1.6k • written 19 months 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
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 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
2
replies
1.8k
views
long computing time for TSS enrichment score
ATACSeq
updated 19 months ago by • 0 • written 2.5 years ago by • 0
0
votes
2
replies
1.5k
views
mogsa on RNA-seq and ATAC-seq data
mogsa atacseq
updated 6.7 years ago by • 0 • written 6.8 years ago by ▴ 30
0
votes
2
replies
1.5k
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
5.9 years ago tangming2005 ▴ 200
0
votes
1
reply
832
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
1
reply
573
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
2
votes
1
reply
3.6k
views
DiffBind on ATAC seq data
ATACSeq
updated 24 months ago by ★ 5.2k • written 24 months ago by ▴ 20
1
vote
1
reply
1.9k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.4 years ago by ★ 5.2k
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
0
votes
1
reply
1.8k
views
Diffbind analysis of ATAC-seq data
ATACSeq DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
votes
1
reply
939
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
745
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
13 months ago isaromero8888 • 0
0
votes
0
replies
962
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.6 years ago Sebastian Lewandowski • 0
0
votes
0
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619
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
9 months ago Raghad • 0
0
votes
0
replies
730
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
13 months ago Jawahar • 0
0
votes
0
replies
732
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
0
replies
904
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
0
replies
828
views
[ATACseqQC] NA values in sigs makes heatmap not completed
ATACseqQC ATACSeq
3.0 years ago hyjforesight • 0
0
votes
0
replies
424
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
11 months ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
217
views
diffbind covariates
DiffBind ATACSeq
updated 4 months ago by 43k • written 4 months ago by ▴ 220
0
votes
0
replies
516
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
14 months ago inna.gur • 0
45 results • Page 1 of 1
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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