User: Macspider
Macspider • 3.3k
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Posts by Macspider
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... 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
Macspider • 3.3k
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... 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)
...
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... Isn't clusterProfiler mostly for mice and human? As far as I remember from their manual. ...
written 8 weeks ago by
Macspider • 3.3k
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... 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
Macspider • 3.3k
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... 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
Macspider • 3.3k
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... 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 ...
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... 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
Macspider • 3.3k
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... 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
Macspider • 3.3k
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... Did you `relevel()` the columns after removing the `Lab` samples? ...
written 10 weeks ago by
Macspider • 3.3k
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... 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
Macspider • 3.3k
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For Why does bcftools call show variants with genotype 0/0 ?
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For A: How to convert .bed file to .juncs file using Tophat?
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5 months ago,
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For Converting blastn output to VCF (for SNPs): what is the quickest way?
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6 months ago,
created a question with more than 1,000 views.
For Best way to compare two samples in a VCF file
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6 months ago,
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For Best way to compare two samples in a VCF file
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For How to retrieve Blast nr database dimensions?
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For HTSeq not counting all the fragments it should count on a gene
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12 months ago,
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For HTSeq not counting all the fragments it should count on a gene
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12 months ago,
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For Why does bcftools call show variants with genotype 0/0 ?
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For Insert size selection for RNASeq data: does it make sense?
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For Quality, MQ0F, other parameters for proper VCF filtering
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15 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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15 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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15 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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17 months ago,
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For Quality, MQ0F, other parameters for proper VCF filtering
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17 months ago,
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For Quality, MQ0F, other parameters for proper VCF filtering
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17 months ago,
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For Quality, MQ0F, other parameters for proper VCF filtering
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18 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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22 months ago,
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For Remove duplicates from reads: best practices?
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23 months ago,
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For A: How to convert .bed file to .juncs file using Tophat?
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