Bioconductor KaryoploteR

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225

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TxDb.Mmusculus.UCSC.mm10.ensGene TxDb karyoploteR

8 days ago • updated 7 days ago remi-xavier.coux ▴ 10

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651

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GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene

19 months ago Shreyash ▴ 10

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1.8k

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BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome

updated 2.2 years ago by James W. MacDonald 67k • written 2.2 years ago by rtt100 • 0

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1.0k

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KaryoploteR

updated 4.3 years ago by Kevin Blighe ★ 4.0k • written 4.3 years ago by mpigozzi • 0

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3.4k

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karyoploter

updated 5.3 years ago by bernatgel ▴ 150 • written 5.3 years ago by Aditya ▴ 160

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1.1k

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karyoploteR

updated 5.6 years ago by bernatgel ▴ 150 • written 5.6 years ago by saeed Ur Rehman • 0

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2.1k

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software error R bsgenome karyoploter

updated 7.1 years ago by bernatgel ▴ 150 • written 7.1 years ago by kirannbishwa01 ▴ 20

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1.4k

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karyoploter

updated 7.2 years ago by bgel ▴ 10 • written 7.2 years ago by spr ▴ 10

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1.0k

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KaryoploteR

7.4 years ago Radek ▴ 90

9 results • Page 1 of 1

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Comment: Differential Expression Genes as Independent Variables by abadgerw • 0

Thanks! I was thinking about this but do not believe glmnet allows for regularized mixed models unless I am mistaken?

Comment: lfcShrink and alpha value by cropero • 0

Thank you for your fast answer, I have everything clear now

Answer: DESeq2 - Comparing Comparisons by James W. MacDonald 67k

Assuming that WC in your equation #2 is different in KD1 subunit1_vs_WC and SCR subunit1_vs_WC, this is just an interaction, and the easies…

Comment: Differential Expression Genes as Independent Variables by James W. MacDonald 67k

An alternative to that is to use the `glmnet` package to fit a regularized regression using all proteins at once.

Comment: Differential Expression Genes as Independent Variables by abadgerw • 0

Thanks. The proposal was not to include all proteins as covariates in one model but to iterate with one protein serving as the independent …

Votes

A: How to bin a GRanges to small bins

C: How to bin a GRanges to small bins

A: deseq2 filter the low counts

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