User: Aaron Lun

gravatar for Aaron Lun
Aaron Lun25k
Reputation:
24,680
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Trusted
Location:
Cambridge, United Kingdom
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
5 years, 2 months ago
Email:
i******************************@gmail.com

I am a research associate in the field of computational biology at the Cancer Research UK Cambridge Institute in the United Kingdom. I am the author and maintainer of the csaw, diffHic, InteractionSet, scrancydar, beachmat, DropletUtils, chipseqDB and simpleSingleCell packages; a co-author and co-maintainer of the scater, SingleCellExperiment and iSEE packages; a co-maintainer of the edgeR package; a co-author of the TENxBrainData package; and an occasional contributor to the limma package.

Posts by Aaron Lun

<prev • 2,678 results • page 3 of 268 • next >
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Answer: A: DE analysis for 10X scRNA-seq data with multiple conditions and multiple replica
... https://osca.bioconductor.org/multi-sample-comparisons.html ...
written 9 weeks ago by Aaron Lun25k
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Comment: C: analysis of multiple batches and multiple treatment conditions in scRNA-seq
... If you have a new question, please ask a new question. ...
written 10 weeks ago by Aaron Lun25k
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Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
... If you can assume that the effect of temperature variation is additive with respect to the other terms, then you can just add it to the design matrix. If you want to identify allele-specific effects of temperature variation, then you would probably have to set up a more complex model with a `allele ...
written 11 weeks ago by Aaron Lun25k
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Answer: A: Correct use of TMM / normalization factors based on large bins
... So close. The effective library size is `library.size * norm.factor`. This means that you should divide your count/coverage/etc. value by `library.size * norm.factor / 1e6` to get normalized per-million equivalents. ...
written 11 weeks ago by Aaron Lun25k
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Comment: C: emptyDrops identified less non-empty cells with lower total UMI counts?
... Well, y'know, back in my day, we didn't have fancy droplet methods for scRNA-seq. We had microwell plates. Plates, and a pipette, for the entire lab. And we had to share the pipette! More seriously, all of the data in the paper was taken from plate-based methods (or close to it, e.g., C1), where we ...
written 11 weeks ago by Aaron Lun25k
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Answer: A: emptyDrops identified less non-empty cells with lower total UMI counts?
... `lower` is used to estimate the "expression" profile of the ambient pool; changing `lower` just means that you're using more-or-less low-count libraries to do this estimation. Provided all of the low count libraries are empty droplets, the ambient proportion estimates should not change much from usi ...
written 11 weeks ago by Aaron Lun25k
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Comment: C: Using edgeR or DESeq2 to analyze allele-specific expression?
... That formulation is not of full column rank. You could drop `alleleM` to get to full column rank, but the coefficients require some more work to interpret: - `individualX:timeY` represent the blocking factors as before. - `alleleP` represents the paternal/maternal log-fold change **at time 1**. Thi ...
written 12 weeks ago by Aaron Lun25k
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Comment: C: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... No, because you don't want to capture the variance due to the batch effect. Recall that `denoisePCA()` operates by assuming that the technical noise is random and occupies the later PCs that are ultimately discarded. A batch effect is not random and will likely occupy one of the very early (often t ...
written 12 weeks ago by Aaron Lun25k
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Answer: A: Is magrittr "%>%" acceptable in bioc packages?
... Ah, that's a raw nerve right there. This question is better placed in the [Bioc-devel mailing list](https://stat.ethz.ch/mailman/listinfo/bioc-devel), which is where all topics of discussion for package development should go. The support site is intended for users to ask questions about... well, u ...
written 3 months ago by Aaron Lun25k
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Comment: C: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... > In the vignette, however, multiBatchNorm is used with HVGs. Is it? Looks like it's being called with `universe`. > Wouldn't it be valid to use `denoisePCANumber` after `multiBatchPCA` with `var.tech` and `var.total` computed by taking grand means instead of means? I thought that too, see ...
written 3 months ago by Aaron Lun25k

Latest awards to Aaron Lun

Scholar 3 months ago, created an answer that has been accepted. For A: scran: excluding genes with extremely high expression during normalization?
Scholar 3 months ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 3 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 3 months ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 3 months ago, created an answer that has been accepted. For A: Time course experiment using limma with voom
Scholar 3 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 3 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Scholar 3 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to identify real cells in 10X RNA-seq ?
Scholar 3 months ago, created an answer that has been accepted. For A: How to identify real cells in 10X RNA-seq ?
Scholar 3 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Scholar 4 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Complex multifactorial design with random effects in Limma/voom
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering for ATAC-seq
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: scRNA-seq : Classification of cell cycle phase
Appreciated 10 months ago, created a post with more than 5 votes. For A: differential expression analysis of htseq data with edgeR/voom
Scholar 10 months ago, created an answer that has been accepted. For A: scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_l
Appreciated 10 months ago, created a post with more than 5 votes. For A: Understanding contrasts limma
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: goana limma- extract list of DE genes and genes in the enriched GO terms?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: EdgeR - blocking for multiple factors at once - Errors
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: applying voom + limma to a block factor design in RNA-seq experiment

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