Bioconductor OrganismDb

Showing : OrganismDb • reset

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OrganismDb AnnotationForge

10 months ago Ozan • 0

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clusterProfiler OrganismDb

updated 17 months ago by Guido Hooiveld ★ 4.1k • written 17 months ago by Aastha Kapoor • 0

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AnnotationForge OrganismData OrganismDb

22 months ago abhisek001 • 0

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annotation organismdb

updated 8.7 years ago by Martin Morgan 25k • written 8.7 years ago by Guido Hooiveld ★ 4.1k

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annotationhub organismdb orgdb unsupported organisms

updated 9.2 years ago by Valerie Obenchain ★ 6.8k • written 9.3 years ago by Guido Hooiveld ★ 4.1k

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promoter granges refseq ucsc organismdb

updated 9.4 years ago by Robert Castelo ★ 3.4k • written 9.4 years ago by efoss ▴ 10

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GO OrganismDb ggbio GO OrganismDb ggbio

updated 10.4 years ago by dalloliogm ▴ 50 • written 10.7 years ago by Georg Otto ▴ 120

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annotationdbi annotation organismdb loadnamespace

10.5 years ago milorobertsmith • 0

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go annotation organismdb

updated 10.5 years ago by James W. MacDonald 68k • written 10.5 years ago by Guido Hooiveld ★ 4.1k

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organismdb annotationdbi annotationforge

updated 10.6 years ago by Marc Carlson ★ 7.2k • written 10.6 years ago by artur ▴ 80

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Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS

updated 11.4 years ago by Matthias Lienhard ▴ 280 • written 11.4 years ago by Hervé Pagès 16k

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Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO

11.4 years ago Hervé Pagès 16k

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GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS

11.4 years ago Hervé Pagès 16k

13 results • Page 1 of 1

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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0

`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/

Comment: error in ChAMP loading file by janwilseo • 0

Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…

Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0

One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…

Comment: DESeq2 Design controlling for gender by donnycrimson • 0

On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…

Votes

DiffBind; Error: No sites have activity greater than filter value

remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

A: Unbalanced experiment with multiple samples from each patient.

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