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Search took 0.01 seconds. Search: Posts Made By: bigmw
Forum: Academic/Non-Profit Jobs 07-09-2018, 07:17 PM
Replies: 0
Views: 1,741
Posted By bigmw
Research Scientist in Biostatistics/Bioinformatics

UNC Charlotte Dept. of Bioinformatics is seeking a full time research scientist in Biostatistics/Bioinformatics. The incumbent will develop statistical and computational methods for big data...
Forum: Bioinformatics 07-28-2017, 04:09 PM
Replies: 1
Views: 2,412
Posted By bigmw
RNA-Seq pathway or gene-set analysis workflow...

RNA-Seq pathway or gene-set analysis workflow with GAGE/Pathview
https://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

Seqanswer thread...
Forum: Bioinformatics 07-26-2017, 01:08 PM
Replies: 6
Views: 2,337
Posted By bigmw
pathview package is running error-free now with...

pathview package is running error-free now with the latest R/BioC and KEGGgraph:
http://bioconductor.org/checkResults/release/bioc-LATEST/pathview/...
Forum: Bioinformatics 07-20-2017, 10:26 AM
Replies: 6
Views: 2,337
Posted By bigmw
Dear all, Thank you for reporting this issue....

Dear all,
Thank you for reporting this issue. Indeed, I was able to replicate the same problem with the latest R/BioC versions.
I just posted the cause and solution for this problem on bioc support...
Forum: Academic/Non-Profit Jobs 06-26-2017, 09:04 AM
Replies: 1
Views: 1,948
Posted By bigmw
with some update

with some update
Forum: Academic/Non-Profit Jobs 06-25-2017, 02:03 PM
Replies: 7
Views: 2,176
Posted By bigmw
Dario1984, Thanks for the comments and...

Dario1984,
Thanks for the comments and interest. The initial Pathview NSF grant is for 3 years. But this position may be extended depending on our needs. Actually most if not all research staff...
Forum: RNA Sequencing 05-16-2017, 06:48 PM
Replies: 1
Views: 1,612
Posted By bigmw
gage does use the latest data from KEGG if you...

gage does use the latest data from KEGG if you generate gene set data using kegg.gsets() function. However, the reference pathway list could be out of date. The reason you see NA for 80 pathways is...
Forum: Academic/Non-Profit Jobs 04-24-2017, 09:30 AM
Replies: 7
Views: 2,176
Posted By bigmw
nilshomer, thanks for understanding. another...

nilshomer,
thanks for understanding. another important factor affecting pay level is the location. People at SF or Boston may be paid substantially higher than other places (expenses there are much...
Forum: Academic/Non-Profit Jobs 04-22-2017, 05:11 PM
Replies: 7
Views: 2,176
Posted By bigmw
nilshomer, Thank you for your frank comments. I...

nilshomer,
Thank you for your frank comments. I understand what you say. I know it is hard to compete with industry in terms of pay level. Academic jobs are quite different and can be appealing in...
Forum: Academic/Non-Profit Jobs 04-21-2017, 05:08 PM
Replies: 7
Views: 2,176
Posted By bigmw
It is still open.

It is still open.
Forum: Bioinformatics 03-01-2017, 01:53 PM
Replies: 8
Views: 3,114
Posted By bigmw
To use custom gene set data as in your case, the...

To use custom gene set data as in your case, the simplest way to go is read in your annotation data file into R and process it into gene set data.
You may use read.delim function to read in data,...
Forum: Bioinformatics 02-27-2017, 04:41 PM
Replies: 8
Views: 3,114
Posted By bigmw
What species you are working on? Gage package can...

What species you are working on? Gage package can generates gene set data for many species (3000 for KEGG and 19 for GO) via some dedicated functions. For details, check:
?kegg.gsets
?go.gsets
Forum: Bioinformatics 12-22-2016, 07:40 PM
Replies: 4
Views: 2,203
Posted By bigmw
Compound data and gene data are two different...

Compound data and gene data are two different types, and are represented differently in pathway graphs. they cannot convert to each other.
Forum: Bioinformatics 12-21-2016, 06:24 PM
Replies: 6
Views: 2,892
Posted By bigmw
Pathview Web server was updated substantially in...

Pathview Web server was updated substantially in the last few months. Please check the main post above for details.
The server is online at http://pathview.uncc.edu/.
Forum: Bioinformatics 12-20-2016, 05:27 AM
Replies: 4
Views: 2,203
Posted By bigmw
sbcn, There are a few general pathways in KEGG,...

sbcn,
There are a few general pathways in KEGG, like 01100, 01200 etc. they are not really classical pathways. Gene/protein nodes on these diagrams are edges instead of nodes, for example:...
Forum: Academic/Non-Profit Jobs 12-01-2016, 05:47 PM
Replies: 1
Views: 1,948
Posted By bigmw
Biostatistics/Bioinformatics Research Scientist

UNC Charlotte Dept. of Bioinformatics is seeking a full time research scientist in Biostatistics/Bioinformatics. The incumbent will develop statistical/computational methods/tools for high throughput...
Forum: Academic/Non-Profit Jobs 12-01-2016, 05:41 PM
Replies: 7
Views: 2,176
Posted By bigmw
Full Time Bioinformatics Software Developer

UNC Charlotte Dept. of Bioinformatics is seeking a full time Software Developer (research associate). The incumbent will lead the development of bioinformatics web servers, resources and...
Forum: Academic/Non-Profit Jobs 08-03-2016, 06:41 PM
Replies: 0
Views: 1,229
Posted By bigmw
Postdoc in Bioinformatics/Biostatistics at UNC Charlotte, NC, USA

The Luo group at UNC Charlotte Dept. of Bioinformatics is seeking a new member as a postdoc researcher. The new members will develop statistical/computational methods/tools for high throughput omics...
Forum: Academic/Non-Profit Jobs 08-03-2016, 06:35 PM
Replies: 0
Views: 813
Posted By bigmw
Bioinformatics Postdoc or Software Developer at UNC Charlotte, NC, USA

The Luo Group at UNC Charlotte Dept. of Bioinformatics is seeking a Bioinformatics Postdoc or Software Developer. The new member will lead the development of bioinformatics web servers and...
Forum: Bioinformatics 05-20-2016, 07:06 AM
Replies: 6
Views: 1,840
Posted By bigmw
As I said above, these few ones are all general...

As I said above, these few ones are all general pathways. They are usually the biggest and most inclusive pathway definitions. Therefore, you get most of your protein mapped. But this never means...
Forum: Bioinformatics 05-08-2016, 03:12 PM
Replies: 6
Views: 1,840
Posted By bigmw
Pathway 01110 is one of the few general pathways,...

Pathway 01110 is one of the few general pathways, which are very different from the regular ones. For instance, genes/proteins in these pathways are edges instead of nodes (rectangles)....
Forum: Bioinformatics 02-23-2016, 12:42 PM
Replies: 6
Views: 2,892
Posted By bigmw
If you are sure that your species is valid, you...

If you are sure that your species is valid, you should check the gene/compound ID type or the input data type (gene or compound). If you specify these options wrong, you may get that error too.
Forum: Bioinformatics 02-20-2016, 01:18 PM
Replies: 6
Views: 2,892
Posted By bigmw
Not sure exactly what happened. But most likely,...

Not sure exactly what happened. But most likely, you did not specify the right data type, species or gene/compound ID type. Did you see any error message?
Forum: Bioinformatics 01-07-2016, 09:50 AM
Replies: 6
Views: 2,892
Posted By bigmw
For more info on Pathview: R/BioC package: ...

For more info on Pathview:
R/BioC package:
http://bioconductor.org/packages/pathview/
Paper:
http://bioinformatics.oxfordjournals.org/content/29/14/1830.full
Forum: Bioinformatics 01-06-2016, 05:53 PM
Replies: 6
Views: 2,892
Posted By bigmw
Pathview Web Server: user friendly pathway visualization and data integration

Dear all,
We are happy to announce that Pathview Web server. It is online at http://pathview.uncc.edu/ since 2016. It was updated substantially in the last few months.

Pathview is a tool set we...
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