> ## Documentation Index
> Fetch the complete documentation index at: https://biobase.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

# Viewers

> Which file types open in a BioBase viewer, and the limits every viewer shares.

Select a file in the file explorer to open it in a pane. Research formats open in a viewer, and other text files open in the editor.

| File type | Extensions | Opens in |
| - | - | - |
| Genome tracks | .bed, .gff, .gff3, .gtf, .vcf, .wig, .bedgraph | [Genome viewer](/viewers/genome) |
| Sequences | .fa, .fasta, .fna, .ffn, .faa, .frn | [Sequence viewer](/viewers/structures-and-sequences) |
| Molecular structures | .pdb, .cif, .mmcif, .sdf, .mol, .mol2, .xyz | [Structure viewer](/viewers/structures-and-sequences) |
| Spreadsheets | .xlsx, .xls | [Spreadsheet viewer](/viewers/tables-and-arrays) |
| CSV and TSV | .csv, .tsv | [Table view](/viewers/tables-and-arrays) in the editor |
| NumPy arrays | .npy, .npz | [Array viewer](/viewers/tables-and-arrays) |
| HDF5 and AnnData | .h5, .hdf5, .h5ad | [HDF5 viewer](/viewers/tables-and-arrays) |
| R objects | .rds, .RData, .rda | [R object viewer](/viewers/tables-and-arrays) |
| Python pickles | .pkl, .pickle, .joblib | [Pickle viewer](/viewers/tables-and-arrays) |
| Charts | .json files holding a Vega-Lite spec | [Chart viewer](/viewers/documents-and-reports) |
| HTML reports | .html, .htm | [Report viewer](/viewers/documents-and-reports) |
| Word documents | .docx | [Document viewer](/viewers/documents-and-reports) |
| PDF | .pdf | [PDF viewer](/viewers/documents-and-reports) |
| Images | .png, .jpg, .jpeg, .gif, .webp, .svg, .bmp, .ico | [Image viewer](/viewers/documents-and-reports) |

A .json file that isn't a chart spec shows as plain text.

## Preview and Source

A text-based research file, such as a FASTA, BED or HTML file, opens in **Preview**. Select **Source** to edit it as text. Preview redraws from your unsaved edits. Binary formats open in **Preview** only.

## How BioBase picks a viewer

BioBase reads the first bytes of a binary file, so PNG, JPEG, GIF and WebP images, HDF5 files, NumPy arrays, uncompressed R objects and pickles written with protocol 2 or later open in the right viewer under any extension. A .json or .html file opens as a chart or a report when its contents are a Vega-Lite spec or an HTML document. Every other format opens by its extension.

## Size limits

| Files | Largest file that previews |
| - | - |
| Research formats in the viewers | 25 MB |
| PDFs and images | 50 MB |
| CSV, TSV and other text files | 50 MB |

A larger file shows "Unable to load file" with its size and the limit. Open it in another application.

## Messages

"BioBase cannot display this format. Open the file in a compatible application." BioBase has no viewer for the format. This covers legacy .doc files, compressed files such as .csv.gz, .xz and .bz2 (a gzip-compressed R object opens), BAM, CRAM, bigWig, bigBed and any other binary format BioBase doesn't recognize. An unrecognized binary file larger than 25 MB shows a binary-file notice instead. FASTQ and GenBank files open as text in the editor.

"This file is password protected. Remove the password in the application that created it, then open the unprotected copy here." The workbook or document is sealed with a password, and BioBase never asks for it. A password-protected PDF reads "This PDF is password-protected" instead.

"This file is empty." The file has no content.

The selected sheet, sequence view and genome assembly reset each time a file opens.


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