Biostar SpikeIn

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DESeq2 SpikeIn Normalization

updated 10 days ago by Michael Love 39k • written 10 days ago by kalavattam • 0

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313

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DiffBind SpikeIn Normalization ChIP-seq csaw

7 weeks ago • updated 27 days ago spg • 0

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424

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DiffBind ChIPSeq Normalization SpikeIn

16 months ago Drew • 0

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324

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SpikeIn SingleCell

17 months ago mb1996 • 0

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567

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ChIPSeq SpikeIn edgeR Normalization

18 months ago maria.soler • 0

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1.9k

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edgeR SpikeIn RNASeq

updated 9 weeks ago by Bogdan ▴ 660 • written 23 months ago by robert.chen • 0

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1.5k

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CUTandRUN edgeR Normalization SpikeIn ChIPSeq

updated 9 weeks ago by Bogdan ▴ 660 • written 2.3 years ago by Hesh ▴ 10

7 results • Page 1 of 1

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Comment: mas5calls function doesn't work; mirna40cdf problem by James W. MacDonald 62k

Yes. Follow the recommendation in the link that was provided to you by Lori Shepherd.

Comment: mas5calls function doesn't work; mirna40cdf problem by Berna • 0

Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?

Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage by ayabalbaa1990 • 0

Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…

Comment: Combat and dds Object by shaimaa • 0

I used the combat-seq but the deseq complain as its not integer what should i do

Answer: Different summary() and results() values in DeSeq2 by Basti ▴ 540

summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…

Votes

Answer: mas5calls function doesn't work; mirna40cdf problem

Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem

Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data

A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings

Awards • All

Popular Question to Guido Hooiveld ★ 3.5k

Scholar to James W. MacDonald 62k

Commentator to Michael Love 39k