User: Bogdan

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Bogdan570
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570
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Trusted
Location:
Palo Alto, CA, USA
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Last seen:
6 days, 12 hours ago
Joined:
11 years, 11 months ago
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Posts by Bogdan

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normalization of RNA-seq data after over-expressing the transcription factors
... Dear all, talking about the standard normalization methods of RNA-seq data as implemented in limma, edgeR or DeSeq2 : is there any modification we shall do in the normalization method when analyzing the RNA-seq data of these 3 sets of samples : a) control b) over-expressing X protein (Wild Type ...
limma edger deseq2 voom written 28 days ago by Bogdan570 • updated 28 days ago by Aaron Lun24k
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Comment: C: correcting the batch effects in Limma and SVA
... Dear Gordon, if I may add and ask please (on a related topic regarding single cell RNA-seq): would COMBAT and LIMMA be suited for assessing the differential expression between clusters of single cells (that were generated by using 10X Genomics protocols/kits) ? 've noted a tutorial from UC Davis ...
written 28 days ago by Bogdan570
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Comment: C: correcting the batch effects in Limma and SVA
... Dear Gordon, if I may add and ask please (on a related topic): would COMBAT and LIMMA be suited for assessing the differential expression between clusters of single cells (that were generated by using 10X Genomics protocols/kits) ? 've noted a tutorial from UC Davis that propose SVA/COMBAT and L ...
written 28 days ago by Bogdan570
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Comment: C: correcting the batch effects in Limma and SVA
... Thanks a lot, Gordon. Very precious advise ! ...
written 29 days ago by Bogdan570
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6 follow
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correcting the batch effects in Limma and SVA
... Dear all, about correcting the batch effects in **LIMMA and SVA,** 'd appreciate having your comments : assuming that we have a set of RNA-seq data (no treatment, + treatment) in many distinct BATCHES, would the linear model in LIMMA : **design <- model.matrix(~0 + BATCH + Treatment, data=RN ...
limma sva combat written 29 days ago by Bogdan570 • updated 29 days ago by Gordon Smyth38k
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using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
... Dear Aaron, and all, after going over the tutorial for detecting differential expression in scRNA-seq data (https://bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/de.html) thought that I could ask you please : **would the same pipeline (that includes edgeR or ...
limma edger scran scater simplesinglecell written 29 days ago by Bogdan570 • updated 28 days ago by Aaron Lun24k
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Comment: C: scRNA-seq : runPCA() and denoisePCA()
... yes, in my R/BioC installation, i was able to see in the **?plotReducedDim** documentation : **"colour by","shape by", "size by"** (and that is great), not a **"text by"** entry yet ;) ...
written 7 weeks ago by Bogdan570
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Comment: C: scRNA-seq : runPCA() and denoisePCA()
... thank you ! yes, it would be really great to have this info in the package documentation ... thanks ;) ...
written 7 weeks ago by Bogdan570
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Comment: C: scRNA-seq : runPCA() and denoisePCA()
... Dear Aaron, if I may add and ask please : is there is any way to overlay the cluster number on a TSNE plot ? (or to use a specific list of colors for the list of clusters shown on the TSNE plot). thank you ! ...
written 7 weeks ago by Bogdan570
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Comment: C: scRNA-seq : Classification of cell cycle phase
... thank you Aaron ! i am going again over the scRNA-seq tutorials: thank you for adding the tutorial on differential expression ! ...
written 7 weeks ago by Bogdan570

Latest awards to Bogdan

Popular Question 14 days ago, created a question with more than 1,000 views. For Error in GenomeInfoDb:::getDanglingSeqlevels
Popular Question 7 months ago, created a question with more than 1,000 views. For about VCF and BAM files
Popular Question 7 months ago, created a question with more than 1,000 views. For (batch) corrections of RNA-seq data: integrating LIMMA and SVA
Popular Question 7 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 7 months ago, created a question with more than 1,000 views. For edgeR and removeBatchEffect()
Popular Question 7 months ago, created a question with more than 1,000 views. For heatmap of genes based on enriched GO categories
Popular Question 7 months ago, created a question with more than 1,000 views. For heatmap of genes based on enriched GO categories
Popular Question 7 months ago, created a question with more than 1,000 views. For about UCSCtrack in Gviz
Popular Question 7 months ago, created a question with more than 1,000 views. For about MAFTOOLS and MAF files
Popular Question 8 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 10 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 10 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 11 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 11 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 11 months ago, created a question with more than 1,000 views. For about collapsed and expanded vcf file
Popular Question 11 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Voter 12 months ago, voted more than 100 times.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 2.1 years ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 2.1 years ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 2.2 years ago, created a question with more than 1,000 views. For question about Gviz
Popular Question 2.5 years ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 2.5 years ago, voted at least 25 times.
Centurion 3.5 years ago, created 100 posts.

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