Bioconductor NCBI

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477

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Rstudio cDNA ensembldb NCBI

4 months ago R_Page • 0

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751

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RStudio convert ensembldb NCBI

5 months ago j_denton • 0

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627

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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 3.9 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

8.2 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

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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

How am i making the data? I am using the DESeq2 output data which I had generated

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k

Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …

Answer: Citation for edgeR user guide by Gordon Smyth 50k

Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…

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

You are just making up data? What is the point of this exercise?

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

What do you mean by 'the information'? Do you have things in particular that you want?

Votes

Answer: Citation for edgeR user guide

Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)

Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.

Answer: minfi::read.metharray.exp

Comment: Trying to use enrichGO

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