Bioconductor Ncbi

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739

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Rstudio cDNA ensembldb NCBI

11 months ago R_Page • 0

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1.7k

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RStudio convert ensembldb NCBI

updated 7 weeks ago by MauriAndres • 0 • written 12 months ago by j_denton • 0

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793

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getGFF NCBI biomartr biomaRt

3.3 years ago Matan G. ▴ 60

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1.2k

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 4.5 years ago by James W. MacDonald 67k • written 4.5 years ago by chefer • 0

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1.6k

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ontology edger limma ncbi organism package

updated 4.7 years ago by Gordon Smyth 51k • written 4.7 years ago by babak.loghmani ▴ 20

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2.5k

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rsubread ncbi GRCh38 hg38

updated 8.1 years ago by Wei Shi ★ 3.6k • written 8.1 years ago by jan.soderman • 0

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1.6k

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ncbi sra search

8.8 years ago massacomgrao • 0

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3.9k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 8.8 years ago by Hervé Pagès 16k • written 8.8 years ago by gokcen.eraslan ▴ 10

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3.5k

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microarray normalization ncbi

updated 9.5 years ago by James W. MacDonald 67k • written 9.5 years ago by pankajnarula84 ▴ 20

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1.4k

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annotate ncbi url

9.9 years ago reuma • 0

10 results • Page 1 of 1

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Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

Votes

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

Awards • All

Scholar to Haibo Liu ▴ 20