Bioconductor Ncbi

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770

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Rstudio cDNA ensembldb NCBI

12 months ago R_Page • 0

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1.8k

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RStudio convert ensembldb NCBI

updated 11 weeks ago by MauriAndres • 0 • written 13 months ago by j_denton • 0

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806

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getGFF NCBI biomartr biomaRt

3.4 years ago Matan G. ▴ 60

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1.2k

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MakeOrgPackageFromNCBI NCBI SQL AnnotationForge

updated 4.6 years ago by James W. MacDonald 67k • written 4.6 years ago by chefer • 0

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1.6k

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ontology edger limma ncbi organism package

updated 4.8 years ago by Gordon Smyth 52k • written 4.8 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 8.2 years ago by jan.soderman • 0

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1.6k

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ncbi sra search

8.9 years ago massacomgrao • 0

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3.9k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 8.9 years ago by Hervé Pagès 16k • written 8.9 years ago by gokcen.eraslan ▴ 10

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3.6k

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microarray normalization ncbi

updated 9.6 years ago by James W. MacDonald 67k • written 9.6 years ago by pankajnarula84 ▴ 20

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1.4k

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annotate ncbi url

10.0 years ago reuma • 0

10 results • Page 1 of 1

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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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