User: Bogdan

gravatar for Bogdan
Bogdan580
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580
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Trusted
Location:
Palo Alto, CA, USA
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Last seen:
3 months, 4 weeks ago
Joined:
12 years, 3 months ago
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Posts by Bogdan

<prev • 333 results • page 1 of 34 • next >
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Comment: C: analysis of multiple batches and multiple treatment conditions in scRNA-seq
... hi Aaron, i will read again your tutorials : -- on DE : *https://bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/de.html* -- on batch correction : *https://bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/batch.html* aiming to place t ...
written 4 months ago by Bogdan580
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Comment: C: analysis of multiple batches and multiple treatment conditions in scRNA-seq
... Hi Aaron, great to hear from you. It would be awesome to have your opinion on the following question please : after TSNE, considering for instance **cluster_0,** could we combine : a -- **the matrix of cells w/ normalized_expression in cluster-0 in WT_batch1,** **with the matrix of cells w/ norma ...
written 4 months ago by Bogdan580
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Comment: C: the coordinates of exons of RefSeq or ENSEMBL genes
... thank you, Martin ! have a happy weekend ! ...
written 4 months ago by Bogdan580
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analysis of multiple batches and multiple treatment conditions in scRNA-seq
... Dear all, please would you advise us on the following : for example, shall we have 2 batches of scRNA-seq data of 2 conditions : *WT_batch1, WT_batch2, DISEASE_batch1, DISEASE_batch2,* would the following approach be statistically legitimate in order to account/correct for the batch effect : ...
limma edger deseq2 combat scrnaseq written 4 months ago by Bogdan580 • updated 4 months ago by Andrew_McDavid190
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Comment: C: the coordinates of exons of RefSeq or ENSEMBL genes
... thanks a lot, Wei ! looking at the example that you did provide, it works great : x <- getInBuiltAnnotation("hg38") x[1:5,] ...
written 4 months ago by Bogdan580
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the coordinates of exons of RefSeq or ENSEMBL genes
... Dear all, please may i ask a simple question : in BioC, what is the simplest (or the most direct way) to retrieve **the COORDINATES of EXONS for RefSeq or ENSEMBL genes** ? thanks a lot, -- bogdan ...
txdb exons genome written 4 months ago by Bogdan580 • updated 4 months ago by Martin Morgan ♦♦ 24k
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Comment: C: using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-
... ok, wonderful, just wanted to double check and have a professional statistical advice ;) thank you for writing a detailed documentation on assessing the differential expression. ...
written 4 months ago by Bogdan580
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Comment: C: normalization of RNA-seq data after over-expressing the transcription factors
... thanks a lot, Aaron. it is great and very helpful to have your advise ;) ...
written 4 months ago by Bogdan580
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Comment: C: using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-
... Hi Aaron, thank you very much for your help and for the questions. i was referring to "part 6 : Using pseudo-bulk counts" : https://bioconductor.org/packages/release/workflows/vignettes/simpleSingleCell/inst/doc/de.html that describes the analysis on a SMART-seq2 dataset (416B cells). It would ...
written 4 months ago by Bogdan580
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Comment: C: normalization of RNA-seq data after over-expressing the transcription factors
... Hi Aaron, great to hear from you. If I may re-phrase the question please : considering the RNA-seq for a set of 3 treatments : - **(a) control** - **(b) over-expressing X protein (Wild Type) i.e. X_WT** - **(c) over-expressing X protein (Mutant) i.e. X_MUT** I have used limma and ...
written 4 months ago by Bogdan580

Latest awards to Bogdan

Popular Question 4 months ago, created a question with more than 1,000 views. For Error in GenomeInfoDb:::getDanglingSeqlevels
Popular Question 10 months ago, created a question with more than 1,000 views. For about VCF and BAM files
Popular Question 10 months ago, created a question with more than 1,000 views. For (batch) corrections of RNA-seq data: integrating LIMMA and SVA
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 edgeR and removeBatchEffect()
Popular Question 10 months ago, created a question with more than 1,000 views. For heatmap of genes based on enriched GO categories
Popular Question 11 months ago, created a question with more than 1,000 views. For heatmap of genes based on enriched GO categories
Popular Question 11 months ago, created a question with more than 1,000 views. For about UCSCtrack in Gviz
Popular Question 11 months ago, created a question with more than 1,000 views. For about MAFTOOLS and MAF files
Popular Question 12 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 14 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 14 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 14 months ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 14 months ago, created a question with more than 1,000 views. For extracting the genes associated with the clusters
Popular Question 14 months ago, created a question with more than 1,000 views. For about collapsed and expanded vcf file
Popular Question 15 months ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Voter 16 months ago, voted more than 100 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Fwd: edgeR dispersions
Popular Question 2.5 years ago, created a question with more than 1,000 views. For about appending GRANGES
Popular Question 2.5 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 question about Gviz
Popular Question 2.8 years ago, created a question with more than 1,000 views. For gene symbols in Gviz
Supporter 2.8 years ago, voted at least 25 times.
Centurion 3.8 years ago, created 100 posts.

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