User: Abhishek Singh

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20
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New User
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Last seen:
11 months, 2 weeks ago
Joined:
8 years, 5 months ago
Email:
a**************@gmail.com

Posts by Abhishek Singh

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Gene ID to Gene Name/Symbol in loom files
... Hi Aaron, The code that I have put in here is an old version. The new version (for new project) has the edits suggested by you. However, here I am running into trouble with the code. The sce objects work fine (only I get warnings): > symb <- mapIds(org.Hs.eg.db, keys=rownames(sce_1), keyty ...
written 11 months ago by Abhishek Singh20
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Gene ID to Gene Name/Symbol in loom files
... Dear Community,   I am reading a single cell file and processing it along with TSNE. Finally generation of loom files.   The commands that I am using to read file is :     loadSCE <- function(path){ sce <- scater::read10XResults(path) #sce <- normalize(sce) # Data normalizatio ...
scater loomr scopeloomr written 11 months ago by Abhishek Singh20 • updated 11 months ago by Aaron Lun25k
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Comment: C: How to resolve these trendVar() warnings and errors
... Hi Aaron,  Thank you for your reply. May I ask you one additional question,How can I put gene names and not gene IDs while reading and processing the files?   presently, everything is based on gene IDs, however, when I want to see the top 50 genes or so it is better to have gene names/symbols tha ...
written 11 months ago by Abhishek Singh20
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How to resolve these trendVar() warnings and errors
... Dear community, I am trying to compute variance for my single cell experiment using scater and other related packages. I am getting warnnings and I am unable to resolve them.  what I am doing is:   > loadSCE <- function(path){ sce <- scater::read10XResults(path) #sce <- no ...
scran scater singlecellexperiment written 12 months ago by Abhishek Singh20 • updated 12 months ago by Aaron Lun25k
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Comment: C: Time course RNA-seq data with replicates
... Hi, I just have the time series, it is a developmental data set with three replicates for each stage. Thank you for the link.   ...
written 3.0 years ago by Abhishek Singh20
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Time course RNA-seq data with replicates
... Hi, I have RNA seq data for 7 time points with 3 replicates each, I would like to mark genes that are differentially expressed at least at one of the time points. The DESeq manual details about dealing with time series data that have two conditions. In general I would like to have a figure like t ...
deseq2 written 3.0 years ago by Abhishek Singh20 • updated 3.0 years ago by Michael Love26k
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Answer: A: Error in TOMplot (WGCNA)
... Hi,   The reduction in number of genes from 12000 to 3500 did the trick for me. I still don't know the reason but will wait for the authors to reply on this.   ...
written 3.2 years ago by Abhishek Singh20
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Comment: C: Error in TOMplot (WGCNA)
... Yes, the function is certainly using my files and I did not mixed it up with the tutorial files. However, the names are same.   ...
written 3.2 years ago by Abhishek Singh20
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Comment: C: Error in TOMplot (WGCNA)
... Hi, Please  have a look at the updated question. ...
written 3.2 years ago by Abhishek Singh20
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Error in TOMplot (WGCNA)
... Hi, I am getting this error while running TOMplot. TOMplot(plotTOM, geneTree, moduleColors, main = "Network heatmap plot, all genes") Error in .heatmap(as.matrix(dissim), Rowv = as.dendrogram(dendro, hang = 0.1), : row dendrogram ordering gave index of wrong length geneTree and plotTOM were m ...
wgcna tomplot written 3.2 years ago by Abhishek Singh20

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Error in TOMplot (WGCNA)

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