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6
votes
8
replies
2.5k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 7 months ago by • 0 • written 4.5 years ago by ▴ 120
0
votes
0
replies
3.6k
views
Comment: Comment: Bad volcano plot
3.2 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.6k
views
Comment: Comment: What does that dip in the density plot mean from a single cell data analysis?
3.3 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
6.0k
views
Comment: Comment: Which method is the best for using in "dba.count" in Diffbind R package
3.3 years ago by m.sadman.sakib ▴ 120
7
votes
10
replies
6.0k
views
8 follow
Which method is the best for using in "dba.count" in Diffbind R package
ChIP-Seq diffbind
updated 12 months ago by ★ 2.1k • written 5.1 years ago by ▴ 120
8
votes
3
replies
1.6k
views
What does that dip in the density plot mean from a single cell data analysis?
seurat scRNAseq
3.3 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.3k
views
Comment: Comment: Publishing RNA sequencing data analysis scripts on Github before or after Public
3.4 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.3k
views
Comment: Comment: Publishing RNA sequencing data analysis scripts on Github before or after Public
3.4 years ago by m.sadman.sakib ▴ 120
11
votes
5
replies
1.3k
views
Publishing RNA sequencing data analysis scripts on Github before or after Publication?
github
3.4 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
17k
views
Comment: Comment: How to identify cell types using addModuleScore function?
3.4 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
17k
views
Comment: Comment: How to identify cell types using addModuleScore function?
3.4 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
64k
views
Comment: Comment: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
3.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.7k
views
Suggestions for doing differential expression with 10x single cell data (two conditions, 4 replicates each, having 30K cells in each conditions))
edgeR rnaseq singlecellrnaseq deseq2 seurat
3.5 years ago by m.sadman.sakib ▴ 120
2
votes
4
replies
4.6k
views
Recommendation for packages for cell type deconvolution from bulk RNAseq data?
RNA-Seq cell type deconvolution
updated 4.3 years ago by • 0 • written 4.5 years ago by ▴ 120
1
vote
0
replies
2.5k
views
Comment: C: Simple explanation and usage of WGCNA package?
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.5k
views
Comment: C: Simple explanation and usage of WGCNA package?
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.5k
views
Comment: C: Simple explanation and usage of WGCNA package?
4.5 years ago by m.sadman.sakib ▴ 120
1
vote
0
replies
2.5k
views
Comment: C: Simple explanation and usage of WGCNA package?
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
3.5k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
4.6k
views
Comment: C: Recommendation for packages for cell type deconvolution from bulk RNAseq data?
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.3k
views
Comment: C: Recommendation for using limma-voom workflow for ChIPseq analysis. Or other tool
4.5 years ago by m.sadman.sakib ▴ 120
1
vote
2
replies
1.3k
views
Recommendation for using limma-voom workflow for ChIPseq analysis. Or other tool for capturing global histone mark difference?
ChIP-Seq
4.5 years ago by m.sadman.sakib ▴ 120
19
votes
7
replies
2.5k
views
How to avoid hardcoding in R? How to automatize R scripts?
R r programming RNA-Seq ChIP-Seq
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
2.5k
views
Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
2.5k
views
Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
3.5k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.5 years ago by m.sadman.sakib ▴ 120
3
votes
11
replies
3.5k
views
Difference of DiffBind library size normalisation vs DESeq2 library size normalisation
DESeq2 Diffbind ChIP-Seq RNA-Seq normalisation
updated 4.6 years ago by ★ 2.1k • written 4.6 years ago by ▴ 120
0
votes
0
replies
3.5k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
3.5k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
3.5k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
5.8k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.6 years ago by m.sadman.sakib ▴ 120
1
vote
1
reply
5.8k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
5.8k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
5.8k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.2k
views
What is Eigengene value? how they can be calculated for groups of genes in two conditions? How SVD is related to it?
RNA-Seq
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
74k
views
Comment: C: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
4.6 years ago by m.sadman.sakib ▴ 120
1
vote
0
replies
2.9k
views
Answer: A: Error when using ChIPQC package
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
2.1k
views
Comment: C: How can I find the promoter regions that have H3k27me3 in two different groups
5.1 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
7.3k
views
Comment: C: How to calculate eigengenes on arbitrary expression data, not inside WGCNA
5.2 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
6.1k
views
Comment: C: Annotate peaks based on Histone Mark
5.2 years ago by m.sadman.sakib ▴ 120
7
votes
5
replies
4.2k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2 ChIP-Seq ChromHMM MACS2 CHROMHMM
updated 5.4 years ago by ★ 1.1k • written 5.5 years ago by ▴ 120
0
votes
0
replies
3.5k
views
Comment: C: Correlating ChIP-Seq peaks with isoform level expression
5.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
4.2k
views
Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
5.5 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
975
views
Defining bivalent promoters with H3K4me3 and H3K27me3 ChIPseq data
ChIP-Seq
5.5 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
4.2k
views
Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
5.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
899
views
Accurately identifying long non coding RNA from stranded total RNAseq(rRNA depleted)
RNA-Seq alignment sequencing
5.6 years ago by m.sadman.sakib ▴ 120
4
votes
3
replies
5.8k
views
Problem with demultiplexing illumina dual indexed libraries
RNA-Seq next-gen sequencing illumina sequence
updated 5.6 years ago by ★ 2.9k • written 5.6 years ago by ▴ 120
0
votes
0
replies
2.6k
views
Comment: C: How to rescale aggregation plots of different ChIP-seq datasets using ngsplot?
5.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
4.0k
views
Comment: C: Normalizing ChIP-seq Data To Spike-In Control
5.9 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
7.4k
views
Comment: C: How to find out whether Chip-seq peaks falls within promoter or enhancer region
5.9 years ago by m.sadman.sakib ▴ 120
57 results • Page 1 of 2
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