Of course, you are allowed to publish any and all figures from our software. That’s the whole point. The software is meant to create figures and give you results that can be directly published so you can save time and [...]
We submitted our publication with images generated in the ipathwayguide analysis. The journal got back to us and asked for vector images or high resolution tiffs (600-900 dpi), and the font used in the exported images are pixelated when you zoom in. Is there a way to fix this or to change the font in the exported image? Can I set the resolution when I download the image?
Regarding the figures, you need to download them in .SVG format from iPathwayGuide. Any downloadable figure in our software can be downloaded as SVG. The SVG is a scalable vector format that can scale to any size and offers perfect [...]
Can you please share with us how we can analyse ChIP-Seq or CLIP/RIP-seq datasets using iPathwayGuide?
The basics are always the same regarding of the assay. The first step is to map the results of your assays onto genes. The assay can be very different but in most cases you can map the results on genes. [...]
I am trying to do pathway analysis for our -organism of you are working with- data. But I can’t select the organism for that as there is no option to select the organism. Is it possible to get data for this organism analyzed using iPathwayGuide?
iPathwayGuide supports directly human, mouse and rat. For other organisms, you need to first map your genes to orthologs. Many of our users have done this very successfully. Here is an example in which iPathwayGuide was used to make important [...]
The answer here is very similar to the one above. When you change the organism, the annotations will be different. This would be a totally different experiment basically. This is an additional reason for which this has to be a [...]
When you change the p-value, the number of differentially expressed genes will change. That in turn, will change every single results in every single type of analysis performed: GO terms, pathway, upstream regulator, drugs, mechanisms, etc. The results will be [...]
We need to extract the list of all DE genes for each pathway, like what Ingenuity Pathway Analysis (IPA) provides for canonical pathway analysis. So, we wonder whether iPathwayGuide has an option/function to extract the names of all DE genes for each of all identified pathways. If so, would you please advise us? Thanks!
On the Pathways tab, on the right hand side, “pathway details” then “Gene table” then the “+" sign. When you click on that, you will see a table with the genes on the pathway. there you can sort, search for [...]
I submitted a test analysis on your server, but seems like I can not access the results since the page is locked. Would you please let me know what I should do in this regard to open the results of analysis?
On your dashboard, you can click on the little shopping cart and then click on “purchase with balance.” The report will become available right away.
When one shares a report with somebody else, the recipient gets a link and they will be able to access the report and do everything that the owner can do. The owner has the opportunity to decide whether the recipient [...]
Question: I went back to analyses that I had previously paid for, opened them and a warning came up for indicated that the analyses were "deprecated" so I hit the re-analyze button only to find that the files are [...]
iPathwayGuide supports analysis of Human, mouse, and rat. It supports the following files formats: CuffDiff DESeq EdgeR SAS/JMP Genomics nSolver (NanoString Technologies) Generic tab delimited .txt file (must contain gene symbol or uniprot ID, log2FC, p-value) SCIEX SWATH 2.0 [...]
Please make sure your are using the "...gene_exp.diff" file that comes from CuffLinks. There are some applications that claim to emulate CuffDiff output (e.g. Galaxy). If you are using one of these applications, please make sure the output file has [...]
Generally, each analysis takes about 15 minutes to complete. If there are other analyses queued ahead of yours, it may take a bit longer. You will receive an email as soon as the analysis is complete.
It is a great idea to use the software and explore the capabilities before making a purchase. The way to do this is to create a free account on our web site www.advaitabio.com. Once you create an account, you will [...]