Data Format & Getting Started

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.

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

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 [...]

A 3-column table containing a gene ID/symbol, log2 fold change, and p-value, ideally as a tab-delimited (TSV) file. Official gene symbols for transcriptomics data (microarray, bulk RNA-seq) and gene symbols or uniprot IDs for proteomics data (mass spec) are preferred [...]