Bioconductor NCBI

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479

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Rstudio cDNA ensembldb NCBI

4 months ago R_Page • 0

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754

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RStudio convert ensembldb NCBI

5 months ago j_denton • 0

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628

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getGFF NCBI biomartr biomaRt

2.7 years ago Matan G. ▴ 60

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988

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 3.9 years ago by James W. MacDonald 65k • written 4.0 years ago by chefer • 0

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1.3k

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ontology edger limma ncbi organism package

updated 4.1 years ago by Gordon Smyth 50k • written 4.1 years ago by babak.loghmani ▴ 20

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2.2k

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rsubread ncbi GRCh38 hg38

updated 7.5 years ago by Wei Shi ★ 3.6k • written 7.5 years ago by jan.soderman • 0

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1.4k

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ncbi sra search

8.3 years ago massacomgrao • 0

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3.4k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 8.3 years ago by Hervé Pagès 16k • written 8.3 years ago by gokcen.eraslan ▴ 10

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3.2k

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microarray normalization ncbi

updated 9.0 years ago by James W. MacDonald 65k • written 9.0 years ago by pankajnarula84 ▴ 20

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1.2k

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annotate ncbi url

9.3 years ago reuma • 0

10 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

Awards • All

Teacher to Gordon Smyth 50k