Bioconductor Batch correction

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1.8k

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scrna-seq integration batch correction

updated 4.9 years ago by Aaron Lun ★ 28k • written 5.0 years ago by p.joshi ▴ 40

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1.3k

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methylation ComBat Linear models batch correction AIC

updated 5.1 years ago by Kevin Blighe ★ 4.0k • written 5.1 years ago by lucasmiranda42 • 0

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779

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DESeq2 batch correction

updated 5.1 years ago by James W. MacDonald 67k • written 5.1 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.4 years ago by Rory Stark ★ 5.2k • written 5.4 years ago by rm1238 • 0

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1.1k

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deseq2 differential expression batch correction design

updated 5.5 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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1.7k

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deseq2 differential expression batch correction

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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2.1k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.7 years ago by Vladimir Kiselev ▴ 150 • written 5.7 years ago by hamza_karakurt ▴ 60

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Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0

Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…

Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0

EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…

Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0

Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…

Answer: combining raw counts and estimated counts by O'Brien • 0

It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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