Moderator: Steve Lianoglou

gravatar for Steve Lianoglou
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Denali
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I am currently a Computational Biologist at Denali.

In previous iterations of this life I was:

 

Posts by Steve Lianoglou

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Answer: A: Number and percent of mapped reads from RNA seq analysis.
... Since you're just getting started in the RNA-seq world, it wouldn't hurt to read up on the multitude of tools that [MultiQC](https://multiqc.info/) works with. The example report right under the fold when you start scrolling down is probably exactly what you want. Now you just have to figure out h ...
written 29 days ago by Steve Lianoglou ♦ 12k
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Comment: C: How to analyze RNAseq data with multiple treatment groups and each subject has p
... Is this any different than the question you asked and the subsequent discussion that followed in this post? https://support.bioconductor.org/p/116427/ ...
written 5 weeks ago by Steve Lianoglou ♦ 12k
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Job: Computational Biology / Genomics Internship at Denali Therapeutics
... Interested applicants can [apply through our website](https://denalitherapeutics.com/job?id=1566904). Feel free to send any questions my way (my last name /at\ dnli /dot\ com) and we'll get answers for you. ## Background Denali Therapeutics is dedicated to developing breakthrough therapies for ne ...
genetics job genomics internship written 9 weeks ago by Steve Lianoglou ♦ 12k
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Answer: A: Use of pseudoalignment estimated counmts as input to edgeR and Limma-Voom
... I'm not in Gordon's group, but I'll still offer an answer: Just follow the instructions outlined in the [tximport vignette](http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#use-with-downstream-bioconductor-dge-packages). They provide instructions on how to rol ...
written 11 weeks ago by Steve Lianoglou ♦ 12k
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Comment: C: newSCESet(countData=all.counts) function not working
... You must be following along with an older version of the workflow than the current one (which Aaron linked to). As far as I know, the `newSCEset` stuff has been completely replaced by using `SingleCellExperiment` objects. You should make sure that you are reading the "release" version of these work ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Enable copying Bioconductor AMI to new region
... Oh, sorry. us-west-2, please. Sorry, from the [other linked thread][1] linked above, I was under the impression that if the image was made public (or something(?)) anyone could copy it to any region ... is that not the case? Thanks so much for your help. [1]: https://support.bioconductor.org/p ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Comment: C: Enable copying Bioconductor AMI to new region
... Hi, is it possible to do the same with the latest (3.8 release) AMI? Thanks! ...
written 3 months ago by Steve Lianoglou ♦ 12k
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Comment: C: scRNA-seq: a question about the names of the columns in a Seurat object
... I would advise you to reference the relevant literature ;-) The MNN paper does a comparison against COMBAT and shows their method to be superior, and the Seurat preprint claims their method to be superior to MNN. If it were me, I'd likely ignore COMBAT and take my time with MNN, LIGER, and Seurat ...
written 4 months ago by Steve Lianoglou ♦ 12k
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Answer: A: scRNA-seq: a question about the names of the columns in a Seurat object
... For better or for worse, Seurat isn't a Bioconductor package, so this board is technically not the right/best place to get help on using it. That having been said: You are likely seeing the <ExperimentN>_<barcodeY> column names because the same barcodes are used across samples/expe ...
written 4 months ago by Steve Lianoglou ♦ 12k
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Comment: C: DESeq2: Small treatment group, large control group
... Searching through google with a site:support.bioconductor.org modifier(?) is almost always better than using the search functionality baked into this board. For instance, googling for: unbalanced groups rnaseq site:support.bioconductor.org gets you a few hits: https://support.bioconductor.org/p/9 ...
written 4 months ago by Steve Lianoglou ♦ 12k

Latest awards to Steve Lianoglou

Popular Question 4 months ago, created a question with more than 1,000 views. For Gene level exploratory data analysis from tximport results
Popular Question 4 months ago, created a question with more than 1,000 views. For error in bioconductor installation
Scholar 5 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Scholar 8 months ago, created an answer that has been accepted. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
Teacher 22 months ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Best DEG tool for datasets with FPKM counts?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar 22 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 22 months ago, created an answer that has been accepted. For A: Best DEG tool for datasets with FPKM counts?
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Estimating and removing batch effects from rna-seq dataset
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: when to apply quantile normalization with voom in limma/voom framework with RNA-
Scholar 23 months ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For C: DEseq2 with limited gene set
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: limma experimental design
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Perform limma on a subset of genes of interest
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Filtering after a contrast
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Counting ambiguously mapped reads per feature
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Filtering lowly expressed genes in voom-limma analysis
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: edgeR subsetting DGEList by column/sample
Scholar 3.0 years ago, created an answer that has been accepted. For A: Filtering after a contrast
Scholar 3.0 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
Scholar 3.0 years ago, created an answer that has been accepted. For C: DEseq2 with limited gene set
Scholar 3.0 years ago, created an answer that has been accepted. For A: unable to find Lumi package in R
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