Biostar Scanvcfparam

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3

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VariantAnnotation subset ScanVcfParam

updated 2.1 years ago by Martin Morgan 25k • written 2.1 years ago by Dario Strbenac ★ 1.5k

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variantannotation vcf readvcf filtervcf scanvcfparam

4.8 years ago Didi ▴ 10

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R variantannotation vcf scanvcfparam readvcf

updated 6.0 years ago by Michael Lawrence 11k • written 6.0 years ago by emily.mccann • 0

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VariantAnnotation filterVcf ScanVcfParam vcf writeVcf

updated 6.8 years ago by Martin Morgan 25k • written 6.8 years ago by pau.puigdevall • 0

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Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by priyanka.m • 0

Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.

Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values by wahaha • 0

I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…

Answer: DESeq2 how to specify contrast to test difference of differences by Nicole • 0

The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…

Comment: DESeq2 how to specify contrast to test difference of differences by Nicole • 0

Thank you, @mikelove - that did it! The results make sense now. From my original post, could you clarify what the `group1w.sexfemale` contr…

Comment: Rsamtools is not available for (for R version 4.0.2) by olinares-perdomo • 0

I had the same problem (R 4.2.0) I used BiocManager::install("Rsamtools", force = TRUE) And it is working fine

Votes

Answer: DESeq2 how to specify contrast to test difference of differences

Comment: DESeq2 how to specify contrast to test difference of differences

Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a

Answer: biomaRt error unable to fix: need help troubleshooting

Answer: edgeR : results from goana and kegga functions show opposite sig. p-value

Awards • All

Scholar to Nicole • 0

Teacher to Michael Love 37k