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2
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3
replies
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How to make a read count matrix from multiple bed files generated by ROSE
super-enhancers rose chipseq diffbind H3K27Ac
updated 2.9 years ago by ▴ 40 • written 5.5 years ago by ▴ 130
0
votes
0
replies
1.2k
views
Are the deconvolved gene expression values (already in fraction) from Cibersotx normalized or require any further normalization like TMM?
Cibersortx deconvolution gene expression
4.4 years ago by Researcher ▴ 130
0
votes
3
replies
1.1k
views
Integration of the TCGA's Agilent 244K and Affymetrix data
Gene expression Agilent 244K Affymetrix TCGA
updated 4.4 years ago by ★ 18k • written 4.4 years ago by ▴ 130
4
votes
5
replies
3.2k
views
How to identify cluster membership from the tSNE coordinates?
tSNE dimention reduction dimensionality reduction
updated 4.7 years ago by ★ 29k • written 4.7 years ago by ▴ 130
1
vote
4
replies
4.9k
views
How does AverageExpression() and aggregateData() differ from each other?
Suerat AverageExpression aggregateData
4.7 years ago by Researcher ▴ 130
0
votes
7
replies
4.4k
views
Problem with AverageExpression() in Seurat
Seurat scRNA Seq AverageExpression clusters
updated 4.7 years ago by 12k • written 4.7 years ago by ▴ 130
2
votes
1
reply
1.7k
views
How to convert 10X single nuclear RNA Seq bam file to fastq?
10x Genomics bamtofastq cellranger snRNA
4.9 years ago by Researcher ▴ 130
2
votes
1
reply
1.5k
views
Looking for suggestions if ROSE can handle multiple samples together?
ChIP-Seq ROSE Super Enhancer H3K27Ac
updated 5.1 years ago by ★ 18k • written 5.1 years ago by ▴ 130
1
vote
3
replies
3.6k
views
Unable to convert single cell RNA Seq bam to fastq using cellranger's bamtofastq
single cell cellranger single cell RNA Seq
5.1 years ago by Researcher ▴ 130
3
votes
3
replies
5.1k
views
Is there a way where we can convert TPM to raw read count?
RNA-Seq TPM Read Count Normalization
updated 3.3 years ago by • 0 • written 5.2 years ago by ▴ 130
17
votes
12
replies
4.2k
views
DiffBind to call differential binding of Super-enhancers from ROSE
Super-enhancers ROSE DiffBind chipseq
updated 5.5 years ago by ▴ 170 • written 5.5 years ago by ▴ 130
1
vote
2
replies
1.4k
views
Unsupervised clustering of super-enhancers from Chip Seq data generated from ROSE
ChIP-Seq Super enhancers ROSE peaks H3K27Ac
5.5 years ago by Researcher ▴ 130
6
votes
8
replies
4.8k
views
Are MACS2's summit or DiffBind's summit options are recommended for histone marks like H3K4me3, H3K27me3, H3K27ac and H3K4me1?
ChIP-Seq macs2 diffbind summit histone
updated 5.6 years ago by ★ 2.1k • written 5.6 years ago by ▴ 130
0
votes
10
replies
2.0k
views
Exploring H3K27me3 loss in cancer
ChIP-Seq histone H3K27me3 macs2 diffbind
5.6 years ago by Researcher ▴ 130
0
votes
1
reply
3.0k
views
What are the most important filters provided by Mutect2 and how should we order them based on their priority?
mutect2 somatic variations cancer normal pair
updated 5.6 years ago by 45k • written 5.6 years ago by ▴ 130
1
vote
3
replies
1.5k
views
Gene Regulatory Network from Single-cell RNAseq
scRNA Seq Network bigSCale2 Regulatory Network
5.7 years ago by Researcher ▴ 130
3
votes
8
replies
1.9k
views
Chip Seq data for histone modifications and their respective genomic coordinates
ChIP-Seq TSS promoter enhancer
5.7 years ago by Researcher ▴ 130
1
vote
5
replies
1.6k
views
GO enrichment analysis from peaks to corresponding genes for each MSigDB Oncogenic Signatures or GO IDs using rGREAT
ChIP-Seq rGREAT MSigDB Oncogenic Signatures Genes
updated 5.9 years ago by ★ 18k • written 5.9 years ago by ▴ 130
11
votes
11
replies
10k
views
Predicting survival of cancer patients using glmnet cox
R survival glmnet cox cancer
updated 2.4 years ago by 89k • written 6.0 years ago by ▴ 130
1
vote
8
replies
1.7k
views
Correct approach to identify differential binding in samples (with no duplicates) from two subtypes of a cancer
ChIP-Seq MACS2 Histone
updated 6.0 years ago by 150k • written 6.0 years ago by ▴ 130
0
votes
4
replies
2.4k
views
Chip Seq analysis for H3K27me3,H3K27ac and K4me1 enrichment
ChIP-Seq deeptools
updated 6.0 years ago by ★ 18k • written 6.0 years ago by ▴ 130
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