Hi All,
I work with Bacillus subtilis and I want to perform some GSEA on an RNA-seq data set. Looking at the literature, I've seen that...
16 results in 0.0028 seconds.
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Obtaining gene sets for GSEA
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Question: Mapping an unique KEGG pathway
Hi, sorry for my ignorance. I would like to know how I could check if all the genes of an unique KEGG PATHWAY (e.g. GO:0009718) are present in my genome?... -
KEGG with pathview using CuffDiff data
Hey everybody,
I am a newbie in coding in Bioinformatic and I have a question.
Using a HPC I perform a quality control and... -
GAGE enrichment GO terms, KEGG pathways
Hello,
I am currently trying to find the enriched pathways following a RNAseq analysis using DESeq2, in a plant species where there is no reference... -
pathview failing on metabolic pathways
Dear all,
I am using R package "pathview" to map my data to B.cereus (bce) KEGG networks.
It works very well with... -
How to proceed for Annotation and Characterization of novel miRNA
We have sequenced miRNA of bubaline/buffalo leukocytes. Some novel miRNAs have been obtained.
One example file has been attached.
... -
gage - local data set
Hi,
I am trying to run gage and FGNet with my local list. But I can't seems to make it works.
I have created a gmt file... -
How do you determine which a gene annotation is correct?
Using the program Artemis, I have to get the annotation of one specific gene. I then have to do a blast search on other databases (Ecocyc, KEGG, etc.)... -
pathways differential expression analysis with KO
Hello!
I assigne K0 onthology to my genes from bacteria metatranscriptome. Now I'd like to carry out a differential expression analysis. Obviously,... -
Visualizing number of hits on KEGG map
Hi Everyone,
I'm not sure this is the right place in SEQanswers for this question but I'll give it a go.
I have a list of KO terms and for... -
Download KGML files base on pathway names
Related with this post, I need to download the KGML of a given pathway name (e.g., Acridone alkaloid biosynthesis)
Via API, I know how... -
Parsing ./spoNA.xml file failed, please check the file!
I am trying the pathway analysis from this workflow (1). I recieve error that parsing some file failed! Other question I have is, if it is enough to just... -
Excel List of Locus Tags and Pathways
Hello SeqAnswers Community,
I am working with Clostridium ljungdahlii (a bacteria that can be found in the KEGG) and am interested in generating... -
How to download kgml files programmatically
I need to download kgml file of given EC numbers,don't know how to proceed .
based on kegg http://www.kegg.jp/kegg/xml/
The KGML... -
Can any softwares or tools convert .KGML files(XML edited) to SVG ones?
In the KEGG website, I've downloaded a KGML file which contains all informations of a pathway. But I want to get the vector graphic of the pathway such...
