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ChromHMM 15 State Descriptions (Genic Enhancer)

roadmap epigenomics encode chromhmm written 3.0 years ago by QVINTVS_FABIVS_MAXIMVS • 2.3k • updated 3 months ago by Researcher • 40

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Why Pash 3.0 has been chosen for Roadmap Epigenome?

roadmap epigenomics alignment pash written 4.5 years ago by Saulius Lukauskas • 530 • updated 4.5 years ago by Chris Miller ♦ 21k

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Binning -log10 P signal tracks

roadmap epigenomics bdgcmp macs2 chip-seq -log10 p written 4.5 years ago by Saulius Lukauskas • 530

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Recent Replies

C: Pull number of cells in cluster from seurat object by cook.675 • 0
Thanks so much for this I really appreciate it!
A: value of TLEN not conforming to the SAM specifications by d-cameron • 2.1k
There are many, many SAM files where the content does not conform to the SAM specifications. In ...
A: length of specific sequences from multi fasta file by Mensur Dlakic • 1.2k
I suspect you will get several different solutions. For this one you will need a program called `...
A: May I use NB.MClust package for RNASeq genes clustering instead of samples clust by qian.li10000 • 0
I'm the developer and maintainer of NB.MClust,and just saw your post. Yes, you can use this pac...
C: Gene regulation network analysis mixed with other unrelated events by andres.firrincieli • 110
> TF are mixed with other unwanted events such as growing and tissue > development along th...
C: Number of Tandem and Interspersed duplications by d-cameron • 2.1k
Part of the problem is that many of the germline events are in regions that are difficult to call...
A: deseq2 or edgeR by Gordon Smyth • 960
edgeR and DESeq2 both apply shrinkage to the logFCs, but the default shrinkage applied by edgeR i...
C: Anyone knows how to plot gene model like this? by louiesxscape • 0
I saw this plot in [Allen KD, McKernan K, Pauli C, Roe J, Torres A, et al. (2019) Genomic charact...
A: Gene regulation network analysis mixed with other unrelated events by tujuchuanli • 50
Thank you for your replying, just one further question about fold change. My original thoughts is...
A: selection soft Power in WGCNA by tujuchuanli • 50
Thank you for your wonderful discussion!
C: Is Position In Vcf File 1-Based (First Index Is At 1 Not 0)? by Raygozak • 1.3k
avoid answering something unrelated to the question.
A: How to remove entire rows from seurat object based on cellhash read by cook.675 • 0
Guys I got it! DUHHHH pbs.hashtag <- subset(pbs.hashtag, subset = hash.ID != "Doublet")

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