User: Macspider

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Macspider3.3k
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Posts by Macspider

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Comment: C: How to convert E. coli gene names from biocyc to Ensembl IDs?
... Oh, so it's not me, it's the Ensembl bacteria page that is down. For a second I thought I was crazy. ...
written 7 weeks ago by Macspider3.3k
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How to convert E. coli gene names from biocyc to Ensembl IDs?
... Hi everyone, I'm struggling with something that I couldn't anticipate to be so hard to find. I am very new to the _E. coli_ world, having worked my whole life with plants. Hence, please don't judge if this is common knowledge. I have a list of genes structured like this: > head(Ctrl) ...
ensembl biocyc escherichia coli conversion R written 7 weeks ago by Macspider3.3k • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
... Isn't clusterProfiler mostly for mice and human? As far as I remember from their manual. ...
written 8 weeks ago by Macspider3.3k
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
... Quite the opposite: I'm an experienced programmer in R/python/bash and I would like as much CLI as possible. In the second paragraph of my question I write *"I would need something that works from command line"* because I am not really a web server type of guy (and I have many samples to process) :) ...
written 8 weeks ago by Macspider3.3k
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Answer: A: how can I the unwanted fasta sequences?
... I guess the only reliable way you can do this is to map these sequences against the *BBIP1* gene sequence, and then keep those that don't map. ...
written 8 weeks ago by Macspider3.3k
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Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
... I am working with several *E. coli* samples, for each of which I have a list of hundreds of differentially expressed genes deriving from DESeq2. Besides log 2 fold change and p-value, I also have their expression in TPM and FPKM. I also have the annotated GO terms for each gene. With all these dat ...
go terms escherichia coli gsea rna-seq gene set written 8 weeks ago by Macspider3.3k • updated 18 days ago by Biostar ♦♦ 20
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Comment: C: How I can get all the information of proteins?
... I would suggest you to edit the question adding more details. 1. Which package? 2. What type of information? 3. On what environment? (I guess R) Otherwise the question is way too vague and no one will be able to help you. ...
written 8 weeks ago by Macspider3.3k
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Comment: C: Remove part of headers in FASTA file
... This is a different question, so please post it as such and not as a comment underneath another question. Besides, please have a look whether your desired output is exactly as you want it (e.g. there are whitespaces which I believe you don't want in there). ...
written 8 weeks ago by Macspider3.3k
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Comment: C: DESeq2: "model matrix is not full rank"
... Did you `relevel()` the columns after removing the `Lab` samples? ...
written 10 weeks ago by Macspider3.3k
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Answer: A: DESeq2: "model matrix is not full rank"
... The issue comes out from here: Sample1 Lab IPSCs Sample2 Lab IPSCs Sample3 Lab IPSCs When you define an interaction term between **Study** and **Stage** you are basically asking the design to be on the groups defined by the combinations of these two columns. In these ...
written 10 weeks ago by Macspider3.3k

Latest awards to Macspider

Good Question 9 weeks ago, asked a question that was upvoted at least 5 times. For Best way to compare two samples in a VCF file
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Explanation of a Perl script
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Why does bcftools call show variants with genotype 0/0 ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 4 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 5 months ago, created a question with more than 1,000 views. For Converting blastn output to VCF (for SNPs): what is the quickest way?
Popular Question 6 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Popular Question 6 months ago, created a question with more than 1,000 views. For Best way to compare two samples in a VCF file
Popular Question 7 months ago, created a question with more than 1,000 views. For How to retrieve Blast nr database dimensions?
Popular Question 8 months ago, created a question with more than 1,000 views. For HTSeq not counting all the fragments it should count on a gene
Popular Question 12 months ago, created a question with more than 1,000 views. For HTSeq not counting all the fragments it should count on a gene
Popular Question 12 months ago, created a question with more than 1,000 views. For Why does bcftools call show variants with genotype 0/0 ?
Popular Question 15 months ago, created a question with more than 1,000 views. For Insert size selection for RNASeq data: does it make sense?
Popular Question 15 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Scholar 15 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Scholar 15 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 17 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 17 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Popular Question 17 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Scholar 18 months ago, created an answer that has been accepted. For A: How to convert .bed file to .juncs file using Tophat?
Popular Question 19 months ago, created a question with more than 1,000 views. For Quality, MQ0F, other parameters for proper VCF filtering
Great Question 22 months ago, created a question with more than 5,000 views. For Remove duplicates from reads: best practices?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How to convert .bed file to .juncs file using Tophat?

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