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Elisabeth Gasteiger
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mathavanbioinfo
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Recent Replies
Comment: Create de novo repeat library
by
evoecogen
▴
20
Are there any alternatives to ProtExcluder? I suddenly started to have problems with v1.2:
The files blastx.out.fnolowm50seqm and blastx.o…
Comment: Find corresponding branch from gene tree in species tree
by
Charlotte West
▴
40
Following your suggestion I've been playing around with Notung and seems like its got a lot of great features. I ran:
```
java -jar notung …
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Lisa
•
0
thanks for your help
Comment: docker build Command Works Yet It Does Not Create A Docker Container
by
Indira
•
0
So - I am trying to get around proxy issues but essentially installing required packages in a docker/sif then trying to use that to run an …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
Ram
38k
Do not add answers unless you're **answering** the top level question. Use `Add Comment` or `Add Reply` instead as appropriate. I've moved …
Comment: Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
by
BioinfoBee
•
0
@juke34 I tried the agat_sp_gxf_to_gff3.pl to sort the gff3 by their chromosome order but doesn't seems to work. Any suggestions?.
Comment: CNV Prediction Tools
by
Quentin M
▴
60
Give a try to [CODEX2][1]
[1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y
Comment: Problem with tximport and plasmodium falciparum
by
bioinfo
▴
20
Thank you. It does not seem to be that. I changed my script a bit.
Now it looks like shown below:
mart <- biomaRt::useMart("protists_…
Comment: Copy Number Variants, where to start?
by
paolo
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60
I have found autoCNV, inCNV, and ClassifyCNV. The second one is for exomic CNVs only, and the third one does not run on Windows, but it mig…
Comment: BLAST reference genome indexing
by
bhumm
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20
Thanks for the explanation and links. So when calling the database in the for use, I call the prefix of all the 'subfiles' which invokes th…
Comment: Averaging across multiple proteomic experiments
by
bhumm
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20
It is two biological replicates. I reasoned it as increasing N=2. For both biological replicates, it is ~13 controls vs ~13 disease conditi…
Comment: How to summarize the expression of a gene when having expression data from diffe
by
i.sudbery
16k
tximport will calculate the weighted effective transcript length, but it doesn't use that in its calculation of gene level expression. Both…
Comment: FATAL: While performing build: build image size <= 0 - Issues With Singularity
by
Indira
•
0
I was building a docker image I created on my computer on an HPC. It seems that due to some network issues I kept getting this FATAL messag…
Answer: Seurat or Bioconductor for single cell RNA seq
by
Lindsey
▴
10
Seurat is an R package, so if you're used to work with other Bioconductor packages, you should be fine! Also the tutorials and manuals from…
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