Bioconductor Ensembldb

Showing : ensembldb • reset

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140

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ensembldb

updated 23 hours ago by James W. MacDonald 65k • written 1 day ago by Fara • 0

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5.5k

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ensembl ensembldb plant arabidopsis thaliana annotationhub

updated 21 days ago by Shiva • 0 • written 5.4 years ago by Guido Hooiveld ★ 3.9k

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156

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ensembldb transcriptome genome coordinateconversion

updated 23 days ago by Michael Love 41k • written 26 days ago by saadmurtazakhan ▴ 10

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216

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TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus

updated 10 weeks ago by James W. MacDonald 65k • written 10 weeks ago by ramonmassoni ▴ 10

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291

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ensembldb genomei GenomeInfoDb

10 weeks ago Kai Hu ▴ 70

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213

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ensembldb biomaRt

updated 10 weeks ago by Robin • 0 • written 11 weeks ago by Pez ▴ 10

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482

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Rstudio cDNA ensembldb NCBI

4 months ago R_Page • 0

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758

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RStudio convert ensembldb NCBI

5 months ago j_denton • 0

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541

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GO ensembldb

6 months ago Rockbar • 0

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819

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AnnotationHubSoftware ensembldb

updated 7 months ago by James W. MacDonald 65k • written 7 months ago by cjag • 0

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biomaRt ensembldb UniProt.ws

updated 6 months ago by Marcel Ramos 690 • written 20 months ago by Recep ▴ 20

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1.3k

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ensembldb

updated 8 months ago by James W. MacDonald 65k • written 8 months ago by Max ▴ 10

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477

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Rsubread ensembldb

updated 8 months ago by James W. MacDonald 65k • written 8 months ago by Ya • 0

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ensembldb biomaRt

updated 9 months ago by Michael Love 41k • written 9 months ago by Benjamin ▴ 30

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ensembldb SNP SNPData genomes

written 2.2 years ago by Weiqiong • 0

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Ensembl Rstudio ensembldb AnnotationHub ensdb

updated 6 weeks ago by shepherl 3.8k • written 2.2 years ago by jon.klonowski ▴ 40

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951

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Annotation biomaRt ensembldb

written 2.4 years ago by Lillian • 0

17 results • Page 1 of 1

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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/

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…

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