User: tospo

gravatar for tospo
tospo40
Reputation:
40
Status:
New User
Location:
United Kingdom
Last seen:
4 months ago
Joined:
4 years, 1 month ago
Email:
f***********@yahoo.de

Posts by tospo

<prev • 13 results • page 1 of 2 • next >
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Capillary sequence trimming algorithm
... I need to implement a quality trimming algorithm for capillary sequence reads (yes, they still exist!) in a Perl package of my own, so I am trying to implement the algorithm used by the PHRED software as well as other tools. There is a description of the Mott algorithm here: https://www.codoncode. ...
capillary sequencing written 4 months ago by tospo40
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Comment: C: How to calculate eigengenes on arbitrary expression data, not inside WGCNA
... BTW: the link to "this paper" doesn't work ...
written 14 months ago by tospo40
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Comment: C: How to calculate eigengenes on arbitrary expression data, not inside WGCNA
... thank you, I will try that! ...
written 14 months ago by tospo40
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How to calculate eigengenes on arbitrary expression data, not inside WGCNA
... I would like to compare the results from different algorithms for clustering data from an RNAseq experiment. One methodology we used is **WGCNA**, which represents each cluster/module by a module **eigengene**. What I am now looking for is a way to calculate such eigengenes on arbitrary lists of g ...
rnaseq wgcna eigengene rna-seq written 14 months ago by tospo40 • updated 14 months ago by Jean-Karim Heriche18k
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Comment: C: When To Use Sed Awk Over Perl Or Python
... you don't need to interrupt your CLI work - check out Perl one-liners (e.g. this great collection) ...
written 3.7 years ago by tospo40
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tophat: importance of mate-inner-distance parameter
... I am confronted with the following problem: at work, a large number of RNAseq libraries have been analysed by an automated pipeline. The pipeline runs tophat to do the mapping. Unfortunately, the mate-inner-distance parameter has been set inconsistently between samples and varies significantly. My ...
rnaseq tophat written 4.0 years ago by tospo40
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topGO use showSigOfNodes for non-topGO data? or: how to visualize GO graph from GOseq
... the topGO package appears to have a function showSigOfNodes, which plots the GO graph and highlights the enriched terms. I have done my GO enrichment analysis with GOseq and that packages doesn't provide a plot function like that. Is there any way the function from topGO can be made to accept the da ...
R bioconductor topgo goseq rna-seq written 4.1 years ago by tospo40 • updated 3.9 years ago by pengchy410
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Answer: A: heatmap.2 RowSideColors ordering problem
... Problems solved, see edit in OP ...
written 4.1 years ago by tospo40
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heatmap.2 RowSideColors ordering problem
... In R heatmap.2 I am supplying my own dendrogram and I want to annotate the columns with colors indicating the grouping of my samples. My data is in DESeq2 objects, so I define a color mapping like this (rld is an rlog transformed DESeqDataSet) sideCols=brewer.pal(12, "Set3")[ as.integer(colData(r ...
R dendrogram heatmap written 4.1 years ago by tospo40
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Comment: C: is it ok to make changes to a DESEq2 object?
... so basically just repeat the dds<-DESEq2(dds) right? I guess it is also ok to change the design formula in this way, right? ...
written 4.1 years ago by tospo40

Latest awards to tospo

Popular Question 3.7 years ago, created a question with more than 1,000 views. For topGO use showSigOfNodes for non-topGO data? or: how to visualize GO graph from GOseq
Popular Question 3.7 years ago, created a question with more than 1,000 views. For heatmap.2 RowSideColors ordering problem
Popular Question 3.7 years ago, created a question with more than 1,000 views. For visualizing RNAseq read coverage in Ensembl genome browser
Popular Question 3.7 years ago, created a question with more than 1,000 views. For tophat: importance of mate-inner-distance parameter
Scholar 4.1 years ago, created an answer that has been accepted. For A: heatmap.2 RowSideColors ordering problem

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