My data is from a non-model organism — how do I analyze it?
There's no built-in path for non-model organisms today; customers have worked around this by mapping their genes to human or another supported organism's orthologs before uploading.
Why am I getting an error telling me to reduce my gene list, even though I already selected “my genes of interest / DE genes only”?
Limiting the number of differentially expressed genes (DEGs) to 5,000 in iPathwayGuide is a deliberate statistical and practical threshold designed to ensure the integrity of your biological analysis. If thousands of genes are flagged as differentially expressed, nearly every pathway [...]
I have Seurat (.rds) files — how do I get them into a format iSCanGuide accepts?
iSCanGuide's native formats are .h5ad and 10x MTX, so Seurat .rds objects need to be converted first. We recommend anndataR, the scverse-maintained R package, which writes .h5ad directly from a Seurat object without requiring a Python environment — SeuratDisk is [...]
Can I upload a multi-sample dataset (e.g., a GEO 10x .tar with several samples) directly into iSCanGuide?
Yes. Untar the archive first, so that each sample sits in its own subdirectory containing that sample's barcodes, features, and matrix files. Then point iSCanGuide at the parent directory holding those subdirectories rather than at an individual sample. All of [...]
My upload or batch submission to iPathwayGuide failed without a clear reason — what should I check?
A few common causes: non-numeric or missing values in the P-Value or Fold Change columns (for example, a "." or blank cell instead of a number) will cause a failure; make sure every row has a valid numeric value in [...]
How do I interpret the Enrichment tab results in iSCanGuide?
It depends on which method produced them. By Cell scores each gene set in each cell. iSCanGuide z-scores every gene within the cell, then compares the genes in your selected set against the genes in all the other sets you [...]
My analysis has been processing for a while — is something wrong?
Most analyses in iPathwayGuide complete within 15 minutes, depending on dataset size. If yours has been running noticeably longer, check that you don't have the same report open in more than one browser tab, as that's a known way to [...]
Why does my downloaded figure look different from what I see on screen?
Exported figures are generated at publication-ready resolution, which can look different in size or layout from the on-screen preview. If your download is unexpectedly large, has extra white space, or is missing something visible on screen, that's a known issue [...]
What format should my Fold Change and P-Value columns be in?
log2(Fold Change) is the standard input, so the Fold Change column should be log2-transformed. iPG can take in raw p-values, and adjusted (multiple-test corrected) p-values, we recommend using adjusted p-values.
Why don’t the numbers in the summary chart match the detail table?
Different views in your report can apply different thresholds, gene subsets, or statistical layers, so the same gene or pathway can show slightly different values depending on which chart or tab you're viewing. If numbers disagree in a way that [...]
What’s the difference between iPathwayGuide, iSCanGuide, iBioGuide, and iKnowledgeBase?
iPathwayGuide performs pathway and functional impact analysis on bulk gene expression data (RNA-seq, microarray, proteomics). iSCanGuide analyzes single-cell and spatial transcriptomics data. iBioGuide is a free life-science literature search engine. iKnowledgeBase is a curated research database for knowledge-driven discovery. iPathwayGuide [...]
What’s a good number of differentially expressed genes to submit for the best results?
We recommend a list of roughly 1,900–2,500 differentially expressed genes for the most interpretable results, though anything under about 5,000 will work well. Lists that are much smaller or much larger than this range can make pathway impact scores harder [...]
Do you support organisms other than human, mouse, and rat?
Our knowledgebase contains databases (e.g., gene sets, pathways) for human, mouse, and rat. Scientists who wish to use our platform for a species not on this list, must first map the genes from the organism of interest to the orthologs [...]
I uploaded the wrong data or discovered an error in my input after running an analysis — can I redo it without using another credit?
If the input data itself was wrong (not just a setting or threshold you'd like to change), contact your Customer Success contact. A manual credit adjustment will be made on a case-by-case basis. There's currently no self-service way to swap [...]
Do you offer a free or no-cost way to try the platform?
Yes — through the iSCanGuide™ Research Access Grant, qualifying applicants get full platform access at no cost (see our Grant FAQ for eligibility). For iPathwayGuide, contact our team to ask about a trial or sample analysis.