User: g.e.novakovsky

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Posts by g.e.novakovsky

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Drug target discovery with single cell RNA-seq
... Hi everyone! Suppose, I have single cell RNA-seq data with two time points: cells at zero time point that are not treated by some drug, cells after the drug treatment. My goal is to identify a mechanism of action of this drug (its targets). Is there any good way of how I can do it? I was thinking a ...
scrna-seq drug target written 7 weeks ago by g.e.novakovsky20
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mitochondrial/ribosomal protein genes in scRNA-seq analysis
... Hi everyone, According to this [tutorial][1], during the first steps of scRNA-seq analysis (normalization, dimensionality reduction, and finding DE genes), you should remove all mitochondrial/ribosomal protein genes. But I also heard from other experts that it's a bad idea and you should not do i ...
scrna-seq data processing rna-seq written 8 weeks ago by g.e.novakovsky20
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Chip-seq data of bivalent regions in hESC
... Hi everyone, Maybe someone knows, is there any published and available Chip-seq data set with all confident bivalent regions (with H3K4me3 and H3K27me3 marks) in human embryonic stem cells, mapped on hg19? ...
stem cells chip-seq hesc written 3 months ago by g.e.novakovsky20 • updated 3 months ago by EagleEye6.2k
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scRNA-seq, filter low expressed genes based on RPKM value
... Hi everyone! I analyze scRNA-seq data set from GEO, and it already comes in RPKM values for each gene in each cell. My aim is to do co-expression analysis with GENIE3, and then do differential expression analysis. So my question is how do you filter low-expressed genes by RPKM values and how do you ...
scrna-seq rpkm expression filtering written 4 months ago by g.e.novakovsky20
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RNA-seq for drug targets
... Hi everyone! Are there any special or classic techniques for finding potential drug targets with RNA-seq analysis? Say, we have 2 conditions (normal and disease) and it's time-series data (4-5 time points). Should we build gene-regulatory networks and look at DE genes/proteins that form connection ...
drug target rna-seq written 5 months ago by g.e.novakovsky20 • updated 5 months ago by Kevin Blighe37k
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GSEA, input metrics
... Hi everyone, I want to run GSEA with my RNA-seq data using fgsea Bioconductor package (http://www.bioconductor.org/packages/release/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html). What metric for gene ranking should I use? Should it be absolute log fold changes or not? In the example, provided ...
gsea rna-seq written 6 months ago by g.e.novakovsky20 • updated 6 months ago by shawn.w.foley180
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Directionality of KEGG/Reactome/Wikipathways
... Hi everyone, Am I right that pathways in KEGG do not have a direction? What I mean by that is for example pathway "KEGG_APOPTOSIS" contains genes that can activate or down regulate apoptosis in cell, am I right? Or is it only those that can activate? What about Reactome/wikipathways? Thanks ...
pathways wikipathways reactome kegg written 6 months ago by g.e.novakovsky20 • updated 6 months ago by h.mon23k
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Transcription factor enrichment analysis
... Hi everyone I am trying to run Fisher exact test for transcription factor enrichment analysis: I have 1017 genes from group A, 44 genes from group B, transcription factor X is present in 440 A genes and 27 B genes. Python fisher exact test: fisher_exact([[27, 440], [17, 577]]) gives 0.02 pvalue, ...
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Pathway enrichment analysis of gene set
... Hi everyone, I have list of genes (differentially expressed for example) and I want to obtain list of enriched pathways (not GO terms), what is the best tool or database to do it? Should I use KEGG or REACTOME database for this purpose or something else? I know, everyone has some preferences here, ...
pathway enrichment analysis written 8 months ago by g.e.novakovsky20 • updated 8 months ago by EagleEye6.2k
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Stringtie output files
... I am a new user of StringTie and probably this question is very simple but I still don't get it... I have my sorted bam files (HISAT2 output, genome v19) and here is my StringTie command (v1.3.4): stringtie hisat2_work/hisat2/alignments.sorted.bam -o stringtie_results/transcripts.gtf -G genes.G ...
gtf stringtie rna-seq written 8 months ago by g.e.novakovsky20 • updated 8 months ago by Kevin Blighe37k

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