Bioconductor Locatevariants

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locatevariants variantannotation genomicfeatures

updated 7.5 years ago by Michael Lawrence ★ 11k • written 7.5 years ago by Lna • 0

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

13 months ago davidhillis • 0

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variantannotation locatevariants

8.7 years ago Jakob Goldmann • 0

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locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation

6.7 years ago Aleksandra • 0

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variantannotation locatevariants metadata mcols

updated 6.4 years ago by Valerie Obenchain ★ 6.8k • written 6.4 years ago by enricoferrero ▴ 660

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txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation

updated 6.8 years ago by Valerie Obenchain ★ 6.8k • written 6.8 years ago by Lna • 0

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variantannotation predict coding locateVariants granges

6.5 years ago tony j • 0

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637

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genomiclocation canonicaltranscripts locateVariants

updated 2.6 years ago by James W. MacDonald 65k • written 2.6 years ago by Paola • 0

8 results • Page 1 of 1

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

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Scholar to James W. MacDonald 65k

Supporter to JKim • 0