User: n.anuragsharma

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Posts by n.anuragsharma

<prev • 14 results • page 1 of 2 • next >
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Parametric or non-parametric tests for qPCR significance testing between treatments?
... When working with qPCR data, the general route to take is to obtain ddCT values by normalising to an internal reference gene followed by subtracting from the mean of the control values. This is followed by raising 2^-(ddCT) to obtain the final gene expression value. We generally work with pooled sa ...
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Comment: C: Looking for a faster way to get doi of pubmed publications
... This is excellent! Yes I primarily use R but somehow had not come across ```rentrez```, and while looking up its vignette I accidentally stumbled across ```RISmed```. Much obliged, thanks! ...
written 7 months ago by n.anuragsharma30
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Comment: C: Looking for a faster way to get doi of pubmed publications
... Thanks! This helps a lot. ...
written 7 months ago by n.anuragsharma30
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Comment: C: Looking for a faster way to get doi of pubmed publications
... I'll check them out thanks. ...
written 7 months ago by n.anuragsharma30
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Looking for a faster way to get doi of pubmed publications
... Is there a faster way to get pubmed doi using an input list of PMIDs? Alternatively is there a way to do all of this in R Bioconductor? import metapub from Bio import Entrez, Medline # Function to get the number of publications matching a query term def pubmed_publications_count(t ...
python bio metapub medline pubmed written 7 months ago by n.anuragsharma30
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Comment: C: What is the simplest way to go from Pubmed ID to citation, programmatically?
... Is there a way to pass a list of pmids instead of looping over a list? It's pretty time consuming when working even with as few as 40,50 publications. ...
written 7 months ago by n.anuragsharma30
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Comment: C: Calculating z-scores using edgeR's fitted values (output of glmQLFit)
... As a continuation, would it be erroneous to average the log2 CPM values of replicates (after I have ascertained that there is indeed greater difference between samples rather than replicates)? ...
written 14 months ago by n.anuragsharma30
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Comment: C: Calculating z-scores using edgeR's fitted values (output of glmQLFit)
... Much appreciated, thank you. ...
written 14 months ago by n.anuragsharma30
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Calculating z-scores using edgeR's fitted values (output of glmQLFit)
... From what I can find in papers, heatmaps using RNA seq data are created in several ways: using log-fold changes, z-scores, etc. The edgeR vignette states: > Inputing RNA-seq counts to clustering or heatmap routines designed for microarray data is not straight-forward, and the best way to do thi ...
R rna-seq edger written 14 months ago by n.anuragsharma30 • updated 14 months ago by Gordon Smyth2.1k
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Creating a score for gene-ontology representation
... I have a group of genes (belonging to a certain development pathway, eg. known to increase trichome number) and their expression data from RNA seq. I have the log2 fold changes of each sample (3 mutants) relative to the control (wildtype) as computed by the edgeR package. I have been tasked with cr ...
R scaling rna-seq normalisation written 14 months ago by n.anuragsharma30 • updated 14 months ago by Jean-Karim Heriche24k

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