Biostar Variantannotation

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VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

written 10.1 years ago by Valerie Obenchain ★ 6.7k

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3.4k

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VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

written 9.1 years ago by Fong Chun Chan ▴ 320

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VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation

written 10.2 years ago by Stephanie M. Gogarten ▴ 840

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421

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RNAseq123 VariantFiltering Alignment VariantAnnotation

updated 4 months ago by James W. MacDonald 62k • written 4 months ago by Mohamed ▴ 10

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375

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R VariantAnnotation

6 months ago rwan.work • 0

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261

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VariantAnnotation

10 weeks ago Stephanie M. Gogarten ▴ 840

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249

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MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation

7 days ago • updated 3 days ago davidhillis • 0

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224

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R VariantAnnotation

6 months ago rwan.work • 0

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vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation

5 weeks ago therealgenna • 0

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Comment: DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2? by Giulia • 0

Hi Rory, Thank you for your quick reply and advice on the matter. The following are the MAplots for the analysis using the background=TRU…

Answer: DESeq2 lfcShrink: swapping reference gives different results for the same compar by ATpoint ★ 2.4k

I asked the same some years back: https://support.bioconductor.org/p/p134551/#p134561

Comment: FlowSOM with unrelated channels by helucro ▴ 70

Could you perhaps comment one why you would want to include non-biological "unrelated" channels such as time and event length for clusterin…

Answer: DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2? by Rory Stark ★ 4.6k

It is unusual to see such a big difference between the two analysis methods, although it is more likely when you have only two replicates d…

Comment: Does DiffBind make consensus peaks sets for samples from a given condition (e.g. by Rory Stark ★ 4.6k

You need to call `dba.normalize()` twice, first to establish the normalization calculations, and the second time to retrieve them: cou…

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Comment: FlowSOM with unrelated channels

Answer: DESeq2 lfcShrink: swapping reference gives different results for the same compar

Answer: Can I run DESeq2 with SMART-Seq data

Comment: RUVSeq and DESeq2 -- all variables in design formula must be columns in colData

A: Compare and filter two BAM files, one record at a time

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Teacher to Michael Love 39k