Bioconductor LiftOver

Showing : liftOver • reset

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liftOver SNP GWASTools

13 months ago bonheur • 0

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1.5k

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lifto liftOver

updated 23 months ago by Marcel Ramos 690 • written 23 months ago by james.dalgleish • 0

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1.6k

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liftOver rtracklayer

updated 3.2 years ago by James W. MacDonald 65k • written 3.2 years ago by Mikhail Dozmorov ▴ 30

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liftOver

updated 3.4 years ago by shepherl 3.8k • written 3.4 years ago by bluepebbles • 0

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liftOver

3.5 years ago geneprophet • 0

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1.2k

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hg19 liftover matrixeqtl DMRcate

updated 4.9 years ago by James W. MacDonald 65k • written 4.9 years ago by yoursbassanio ▴ 10

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rtracklayer export.bw liftover

updated 5.4 years ago by Michael Lawrence ★ 11k • written 5.4 years ago by ang ▴ 20

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1.1k

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rtracklayer liftOver parameters minMatch

updated 6.0 years ago by Michael Lawrence ★ 11k • written 6.0 years ago by Nik dAK ▴ 10

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2.8k

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rtracklayer liftover bioconductor R

updated 6.7 years ago by Michael Lawrence ★ 11k • written 6.7 years ago by m.guelfi • 0

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1.7k

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liftover rtracklayer

updated 6.7 years ago by Michael Lawrence ★ 11k • written 6.7 years ago by beausoleilmo • 0

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software error liftOver workflowinstall package installation

updated 7.6 years ago by James W. MacDonald 65k • written 7.6 years ago by JustGettinStarted • 0

11 results • Page 1 of 1

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Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…

Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

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/

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?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0