Bioconductor Ncbi

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482

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Rstudio cDNA ensembldb NCBI

4 months ago R_Page • 0

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756

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RStudio convert ensembldb NCBI

5 months ago j_denton • 0

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629

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getGFF NCBI biomartr biomaRt

2.7 years ago Matan G. ▴ 60

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990

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 4.0 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

Recent ...

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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…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Votes

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?

Answer: Interpret plot from DiffBind

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0