User: Mike

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Mike1.1k
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Posts by Mike

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Comment: C: How to download/build GRCh37.EBVB95-8wt.ERCC genome / include spike-in genome
... Thanks RamRS, I edited my post ...
written 7 days ago by Mike1.1k
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Comment: C: How to download/build GRCh37.EBVB95-8wt.ERCC genome
... I tried with GENCODE and Ensembl for GRCh37 and build index file. But I do not know how to include the spike-in genome. ...
written 7 days ago by Mike1.1k
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How to download/build GRCh37.EBVB95-8wt.ERCC genome / include spike-in genome
... Hi All, I used GENCODE and Ensembl for build GRCh37 index file. But I do not know how to include the spike-in genome. I want to reproduce my results using "GRCh37.EBVB95-8wt.ERCC" genome but I dont know how to build this genome. Thanks ...
genome sequence rna-seq written 7 days ago by Mike1.1k
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Comment: C: Eigen genes using WGCNA
... This script will give you name of genes in each module ...
written 12 weeks ago by Mike1.1k
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Comment: C: Eigen genes using WGCNA
... Agree with Kevin's point. you can try with this code to extract modules.. **Extract modules** module_colors= setdiff(unique(dynamicColors), "grey") for (color in module_colors){ module=SubGeneNames[which(dynamicColors==color)] write.table(module, paste("module_",color, ".t ...
written 3 months ago by Mike1.1k
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Pipeline for analysis Lexogen QuantSeq 3' mRNA-Seq data
... Hi All, I am looking pipeline for analysis Lexogen QuantSeq 3' mRNA-Seq data. I will be very grateful if you help me. regards ...
rna-seq lexogen 3'rnaseq written 3 months ago by Mike1.1k • updated 9 weeks ago by Biostar ♦♦ 20
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Answer: A: How to convert fasta file format to phylip file format
... I found a nice tutorial to build Phylogenetic Trees from fasta sequence... http://www.cbs.dtu.dk/courses/biosys/binfintro/phylogeny.php Step 1: Open the sequence file (fasta), select the entire file, and copy the sequences. Step 2 : Align the sequences in using the mafft server at EBI with def ...
written 3 months ago by Mike1.1k
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Comment: C: How to convert fasta file format to phylip file format
... Thanks cpad0112, yes I can read file in read.phylip function from phylotools but not from ggtree/ treeio. How can I build tree using this phylip file in phylotools. ...
written 3 months ago by Mike1.1k
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Comment: C: How to convert fasta file format to phylip file format
... Thanks Sej, thats my problem, how to generate phylip file (phylip alignment + newick string) to plotting in ggtree. ...
written 3 months ago by Mike1.1k
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Comment: C: How to convert fasta file format to phylip file format
... Thanks jrj.healey for your help, I have around 150 protein sequences, this is just toy/example data. ...
written 3 months ago by Mike1.1k

Latest awards to Mike

Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Single Cell RNAseq data analysis protocol
Good Question 12 weeks ago, asked a question that was upvoted at least 5 times. For Single Cell RNAseq data analysis protocol
Popular Question 12 weeks ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Scholar 3 months ago, created an answer that has been accepted. For A: survival analysis question
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Popular Question 5 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
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Popular Question 8 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
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Popular Question 12 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
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Popular Question 12 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
Popular Question 12 months ago, created a question with more than 1,000 views. For TCGA data: comparision in normal and tumor samples
Popular Question 12 months ago, created a question with more than 1,000 views. For GSVA analysis in R: How to use my geneset and expression data matrix in GSVA.
Student 12 months ago, asked a question with at least 3 up-votes. For Single Cell RNAseq data analysis protocol
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Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: ChIP-seq. analysis Tutorial for Dummies
Popular Question 14 months ago, created a question with more than 1,000 views. For HTSeq error when reading BAM file
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Popular Question 15 months ago, created a question with more than 1,000 views. For HTSeq error when reading BAM file
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: ChIP-seq. analysis Tutorial for Dummies

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