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6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 10 days ago by • 0 • written 3.9 years ago by ▴ 120
0
votes
0
replies
2.8k
views
Comment: Comment: Bad volcano plot
2.6 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.3k
views
Comment: Comment: What does that dip in the density plot mean from a single cell data analysis?
2.7 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
5.1k
views
Comment: Comment: Which method is the best for using in "dba.count" in Diffbind R package
2.7 years ago by m.sadman.sakib ▴ 120
7
votes
10
replies
5.1k
views
8 follow
Which method is the best for using in "dba.count" in Diffbind R package
ChIP-Seq diffbind
updated 5 months ago by ★ 2.0k • written 4.5 years ago by ▴ 120
8
votes
3
replies
1.3k
views
What does that dip in the density plot mean from a single cell data analysis?
seurat scRNAseq
2.7 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.1k
views
Comment: Comment: Publishing RNA sequencing data analysis scripts on Github before or after Public
2.8 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.1k
views
Comment: Comment: Publishing RNA sequencing data analysis scripts on Github before or after Public
2.8 years ago by m.sadman.sakib ▴ 120
11
votes
5
replies
1.1k
views
Publishing RNA sequencing data analysis scripts on Github before or after Publication?
github
2.8 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
16k
views
Comment: Comment: How to identify cell types using addModuleScore function?
2.8 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
16k
views
Comment: Comment: How to identify cell types using addModuleScore function?
2.8 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
58k
views
Comment: Comment: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
2.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.5k
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
2.9 years ago by m.sadman.sakib ▴ 120
2
votes
4
replies
4.3k
views
Recommendation for packages for cell type deconvolution from bulk RNAseq data?
RNA-Seq cell type deconvolution
updated 3.7 years ago by • 0 • written 3.9 years ago by ▴ 120
1
vote
0
replies
2.1k
views
Comment: C: Simple explanation and usage of WGCNA package?
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.1k
views
Comment: C: Simple explanation and usage of WGCNA package?
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.1k
views
Comment: C: Simple explanation and usage of WGCNA package?
3.9 years ago by m.sadman.sakib ▴ 120
1
vote
0
replies
2.1k
views
Comment: C: Simple explanation and usage of WGCNA package?
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.9k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
4.3k
views
Comment: C: Recommendation for packages for cell type deconvolution from bulk RNAseq data?
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.1k
views
Comment: C: Recommendation for using limma-voom workflow for ChIPseq analysis. Or other tool
3.9 years ago by m.sadman.sakib ▴ 120
1
vote
2
replies
1.1k
views
Recommendation for using limma-voom workflow for ChIPseq analysis. Or other tool for capturing global histone mark difference?
ChIP-Seq
3.9 years ago by m.sadman.sakib ▴ 120
19
votes
7
replies
2.2k
views
How to avoid hardcoding in R? How to automatize R scripts?
R r programming RNA-Seq ChIP-Seq
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
2.2k
views
Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
2.2k
views
Comment: C: How to avoid hardcoding in R? How to automatize R scripts?
3.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
2.9k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
3.9 years ago by m.sadman.sakib ▴ 120
3
votes
11
replies
2.9k
views
Difference of DiffBind library size normalisation vs DESeq2 library size normalisation
DESeq2 Diffbind ChIP-Seq RNA-Seq normalisation
updated 4.0 years ago by ★ 2.0k • written 4.0 years ago by ▴ 120
0
votes
0
replies
2.9k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.9k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
2.9k
views
Comment: C: Difference of DiffBind library size normalisation vs DESeq2 library size normali
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
5.4k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.0 years ago by m.sadman.sakib ▴ 120
1
vote
1
reply
5.4k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
5.4k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
5.4k
views
Comment: C: DESeq2 Appropriate Settings for Poorly Clustering Samples?
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
989
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
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
65k
views
Comment: C: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
4.0 years ago by m.sadman.sakib ▴ 120
1
vote
0
replies
2.7k
views
Answer: A: Error when using ChIPQC package
4.0 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.8k
views
Comment: C: How can I find the promoter regions that have H3k27me3 in two different groups
4.5 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
6.9k
views
Comment: C: How to calculate eigengenes on arbitrary expression data, not inside WGCNA
4.6 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
5.4k
views
Comment: C: Annotate peaks based on Histone Mark
4.6 years ago by m.sadman.sakib ▴ 120
7
votes
5
replies
3.7k
views
Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2 ChIP-Seq ChromHMM MACS2 CHROMHMM
updated 4.8 years ago by ★ 1.1k • written 4.9 years ago by ▴ 120
0
votes
0
replies
3.3k
views
Comment: C: Correlating ChIP-Seq peaks with isoform level expression
4.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
3.7k
views
Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
4.9 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
869
views
Defining bivalent promoters with H3K4me3 and H3K27me3 ChIPseq data
ChIP-Seq
4.9 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
3.7k
views
Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
4.9 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
832
views
Accurately identifying long non coding RNA from stranded total RNAseq(rRNA depleted)
RNA-Seq alignment sequencing
5.0 years ago by m.sadman.sakib ▴ 120
2
votes
3
replies
5.3k
views
Problem with demultiplexing illumina dual indexed libraries
RNA-Seq next-gen sequencing illumina sequence
updated 5.0 years ago by ★ 2.9k • written 5.0 years ago by ▴ 120
0
votes
0
replies
2.5k
views
Comment: C: How to rescale aggregation plots of different ChIP-seq datasets using ngsplot?
5.3 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
3.8k
views
Comment: C: Normalizing ChIP-seq Data To Spike-In Control
5.3 years ago by m.sadman.sakib ▴ 120
0
votes
1
reply
6.5k
views
Comment: C: How to find out whether Chip-seq peaks falls within promoter or enhancer region
5.3 years ago by m.sadman.sakib ▴ 120
57 results • Page 1 of 2
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