BioPeek

Feature Tour

~1 minute tour of key features

◫ Split View

Click Split in the toolbar to display the table and stats side by side. The table takes 2/3 width, with a summary panel on the right showing all computed statistics for the current file.

≠ Diff — Compare Two Files

When two or more files of the same format are open, the Diff button appears. Click it to compare rows between the active file and the next same-format tab. Rows are matched by natural keys:

• VCF: CHROM:POS:REF>ALT
• BED: CHROM:START-END
• FASTA/FASTQ: Sequence ID
• Other: Entire row as key

🔗 Shareable Links

Click Share to generate a URL with the file data encoded directly in the link. Anyone who opens the link sees the file instantly — no server, no upload.

File size limit: 100 KB (larger files would create URLs too long for browsers to handle).

⚠ Anomaly Detection

BioPeek automatically scans files for common data quality issues and highlights affected rows with an amber left border. Hover over a highlighted row to see the anomaly description.

Checks performed per format:

⚠ File Validation Report

When a file is loaded, BioPeek automatically checks for format-level issues (missing headers, wrong column counts, etc.) and shows a validation panel at the bottom if problems are found. This is separate from row-level anomaly detection.

Column Histogram Sidebar

Double-click any column header to open a sidebar showing statistics and a histogram for that column. Numeric columns show min, max, mean, median, and a bar chart distribution. Categorical columns show frequency counts for the top values.

Clipboard Paste & Smart Paste

Paste text directly into BioPeek with Ctrl+V. If the pasted text looks like bioinformatics data (starts with >, @, ##, etc.), it is auto-parsed as a new file tab named pasted-<timestamp>. Useful for quick inspection of sequences from papers or terminal output.

Smart paste auto-detects the format of pasted content. Raw nucleotide sequences without headers are wrapped as FASTA. Tab-delimited rows with chromosome columns are detected as BED. Comma-separated data becomes CSV. No manual format selection needed.

Sequence Selection Tools

Select any DNA/RNA text in the table and a popup appears with:

• Reverse complement — computed client-side
• GC content — percentage of G+C bases
• Codon translation — 3-frame translation to amino acids
• Copy buttons for each result

Sequence Motif Search

Search for DNA/RNA motifs across all sequence columns. Use IUPAC ambiguity codes (e.g., TATAWR for TATA box, CANNTG for E-box) or regex patterns. Matching positions are highlighted inline within sequence cells. The results panel shows match count and positions per sequence.

Codon Coloring for FASTA

FASTA sequence cells display codon-level coloring when a reading frame is selected. Each three-nucleotide codon is tinted by amino acid property: hydrophobic (amber), polar (cyan), positive (violet), negative (rose). Stop codons are marked in red. Toggle codon coloring from the column header context menu on sequence columns.

BLAST Search

Right-click any sequence cell (≥ 10 bp) and select "BLAST this sequence" to open NCBI BLAST in a new tab with the sequence pre-filled. Works with FASTA sequences and any column detected as a DNA/RNA sequence.

Format Conversion

The Export dropdown includes format conversion options based on the current file type:

📷 Screenshot Export

Click Screenshot to export the current view as a PNG image. The screenshot includes file name, format, row count, column headers, and up to 30 rows of data. Stats view captures all computed statistics. Screenshots preserve ATCG nucleotide coloring (A=green, T=red, G=amber, C=blue), column auto-sizing, and the current theme (dark/light). The image downloads automatically as a PNG file.

Regex Capture Groups

Type a regex with capture groups (parentheses) in the search box. A floating panel appears showing all matches with extracted groups. Useful for pulling structured data out of free-text columns like VCF INFO or GFF attributes.

Example: searching gene_name "([^"]+)" in a GTF file extracts gene names into a results panel.

☼ Theme Toggle

Click the Theme button in the toolbar to switch between dark and light mode. Your preference is persisted in localStorage and applied automatically on next visit. The theme also applies to screenshots and exported HTML.

Dark theme

Light theme

Column Resize

Hover over the right edge of any column header to reveal a drag handle. Click and drag to resize the column width. The cursor changes to a resize indicator on hover. Column widths are remembered for the current session.

Sort Arrows

Active sort columns display visual indicators in the header: ▲ for ascending and ▼ for descending. The sorted column header is highlighted to make the current sort state immediately visible. Click a column header to cycle through: ascending → descending → unsorted.

Ascending

Descending

📌 Pin Columns

Pin any column to keep it visible while scrolling horizontally. Right-click a column header and select Pin Column, or use the Pin Cols toolbar button to pin the first two columns. Pinned columns stay frozen on the left side of the table. You can pin multiple columns independently — not just the first two.

Header context menu

Cell context menu

▾ Inline Column Filters

Each column header has a small filter icon (▾). Click it to open a dropdown showing all unique values in that column. Check or uncheck values to filter the table. Active filters show a highlighted filter icon. Multiple column filters combine with AND logic.

Row Count in Tabs

Each file tab displays a badge showing the number of rows in that file. This gives an at-a-glance size comparison when multiple files are open. The badge updates when filters are applied, showing filtered count vs total (e.g., 234 / 1,089).

Multi-Column Sort

Hold Shift and click additional column headers to sort by multiple columns. Each sorted column shows a priority number (①②③) indicating the sort order. The first-clicked column is the primary sort, second is secondary, and so on. Click a sorted column without Shift to reset to single-column sort.

Column Reorder

Drag any column header to rearrange the column order. A blue insertion indicator shows where the column will be placed. The reordered layout persists for the current session and is included when saving views.

💾 Saved Views

Save the current table configuration (sort order, filters, column order, pinned columns, column widths) as a named view. Views are stored in localStorage and can be restored later. Useful for switching between different analysis perspectives on the same file.

Selection Stats

Hold Ctrl and click rows to select multiple rows. The footer bar updates to show the count of selected rows. Use Space to toggle selection on the focused row. Selected rows can be exported as a subset via the Export menu.

VCF INFO Parser

VCF INFO fields are automatically expanded into individual key=value pairs in the row detail panel. Click a row (with Detail toggle enabled) to see the full INFO field parsed into a readable list. Fields like DP=42;AF=0.5;MQ=60 become separate labeled entries.

Reverse Complement

Right-click any cell containing a DNA/RNA sequence and select Reverse Complement from the context menu. The reverse complement is computed client-side and can be copied to clipboard. Also available via the sequence selection popup (select text in a sequence cell).

GC% Auto-offer

When BioPeek detects a column containing DNA or RNA sequences, it automatically offers to compute GC content. A small GC% badge appears next to the column header. Click it to add a computed GC% column to the table. The GC percentage is calculated as (G+C) / (A+T+G+C) × 100.

Coordinate Jump

Press Ctrl+G to open the "Go to Row" dialog. Type a row number and press Enter to scroll directly to that row. Useful for navigating large files with thousands of rows.

Genomic Coordinate Navigation

Press Ctrl+Shift+G to open the genomic coordinate search. Type a coordinate like chr1:12345 or a range like chr1:10000-20000 and press Enter. BioPeek filters the table to show only rows overlapping that region. Works with VCF, BED, GFF, and SAM files that have chromosome and position columns.

Keyboard Help Overlay

Press ? to display a keyboard shortcuts overlay listing all available hotkeys. The overlay groups shortcuts by category (navigation, selection, view modes, tools). Press Esc or ? again to dismiss.

Recent Files

The BioPeek landing page shows a list of recently opened files. Each entry displays the file name, format icon, file size, row count, and the date it was last opened. Files cached in IndexedDB show a green dot and restore instantly on click. Recent file history is stored in localStorage.

Drag-to-Group

Drag a column header to the group bar area above the table to group rows by that column's values. Grouped rows are collapsible — click the group header to expand or collapse. Group headers show the value and row count. Useful for grouping VCF variants by chromosome or BED features by strand.

Cell Editing

Double-click any cell to edit its value in place. Press Enter to confirm the edit or Esc to cancel. Each edit pushes an undo entry — press Ctrl+Z to revert. Edited cells are highlighted with a subtle border to indicate modifications.

Column Type Override

Right-click a column header and select Change Type to override the auto-detected column type. Options include text, numeric, and sequence. Changing a column to numeric enables statistical functions (min, max, mean); changing to sequence enables GC%, reverse complement, and BLAST tools.

🎨 Tab Colors

File tabs are color-coded by format for quick visual identification when multiple files are open:

Tab Tooltip

Hover over any file tab to see a tooltip with detailed file information: file size, row count, detected format, and data quality score. The quality score reflects completeness (percentage of non-empty cells) and validity (percentage of values passing format checks).

Rename Tab

Double-click a file tab to rename it. Type the new name and press Enter to confirm, or Esc to cancel. The rename is cosmetic only — it does not affect the underlying file.

Duplicate Tab

Right-click a file tab and select Duplicate to create a copy of the tab with the same data. The duplicate tab has an independent sort/filter state, so you can compare different views of the same data side by side.

▣ Fullscreen

Press F11 or click the Fullscreen button to toggle fullscreen mode. In fullscreen, the toolbar and navigation are hidden, giving maximum space to the table. Press F11 or Esc to exit.

Row Number Toggle

Click the Row # button in the toolbar to show or hide the row number column. Row numbers are shown by default but can be hidden to save horizontal space on narrow screens.

Copy Column

Right-click any column header and select Copy Column to copy all values in that column to the clipboard, one value per line. Respects any active filters — only visible rows are copied.

Unique Values

Right-click a column header and select Unique Values to see a popup listing all distinct values in the column with their frequency counts, sorted by count descending. Useful for quick data profiling.

Column Auto-fit

Double-click the column resize handle (right edge of header) to auto-fit the column width to the widest value in that column. Scans visible rows to determine optimal width.

Text Wrap

Click the Wrap toolbar button to toggle word wrapping for long text cells. When enabled, cell content wraps within the cell instead of being truncated with an ellipsis. Particularly useful for GFF attribute columns and VCF INFO fields.

Numeric Formatting

Right-click a numeric column header and select Format to choose how numbers are displayed: fixed decimal places (0–6), scientific notation, or percentage. Formatting is visual only and does not alter the underlying data. Useful for quality scores, p-values, and allele frequencies.

🏭 External Database Links

Right-click cells to open external biological databases in a new tab. BioPeek detects the data type and offers the appropriate link:

Regex Search

The search box supports regular expression patterns. Type a regex pattern and matching rows are highlighted. When the pattern includes capture groups, a floating panel shows extracted matches. For example, AF=([0-9.]+) extracts allele frequency values from VCF INFO fields.

★ Bookmark Rows

Click the Bookmarks toolbar button to reveal a star column. Click the star icon on any row to bookmark it. Bookmarked rows persist for the session. Click the filled star (★) in the header to export only bookmarked rows. Useful for flagging variants of interest during manual review.

Export HTML

From the Export dropdown, select Export as HTML to save the current view as a standalone HTML file with all styling included. The exported file is self-contained (no external dependencies) and can be opened in any browser or shared via email.

◫ Split View — Dual Tab Comparison

Click Split when two or more files are open to enter side-by-side dual-tab comparison mode. Each pane has independent scroll, sort, and filter controls. Useful for comparing different samples or before/after filtering results.

Goto Row

Press Ctrl+G to open the "Go to Row" dialog. Enter a row number to jump directly to it. The target row is briefly highlighted after navigation. Works with both the original row numbers and filtered-view row numbers.

🎨 Conditional Formatting

Right-click a column header and select Conditional Format to color cells based on value rules. Set an operator (equals, greater than, less than, contains, between), a threshold value, and a highlight color. Multiple rules can be applied to the same column. Rules stack in order — later rules override earlier ones for the same cell.

Find & Replace

Click the Replace toggle next to the search box to expand the find & replace bar. Type the search term and replacement value, then click Replace (single match) or Replace All. Works on text columns only — numeric columns are not modified. Each replacement pushes an undo entry.

Header Sparklines

Numeric column headers display tiny inline SVG histograms showing the value distribution at a glance. The sparkline uses 10 bins and scales to the column header width. Hover over the sparkline to see bin ranges and counts. Sparklines are automatically computed when the file is loaded.

Diff Two Rows

Select exactly 2 rows with Ctrl+click, then click the Diff button (or the "Diff Rows" option that appears). A side-by-side comparison panel opens, with differing cell values highlighted in amber. Identical values are dimmed. Useful for comparing two variants, two sequences, or two samples.

Selection Stats in Footer

Select cells by clicking or Ctrl+clicking rows. The footer bar shows live statistics for the selected data: count, sum, average, min, and max of numeric values in the selection. Non-numeric values contribute to count only.

JSON Cell Expander

Double-click a cell that contains JSON content (detected by leading { or [) to open a formatted, syntax-colored popup. The JSON is pretty-printed with indentation. Collapsible nodes allow exploration of nested structures. Click outside or press Esc to close.

Copy Column Name

Right-click any column header and select Copy Column Name to copy the header text to the clipboard. Handy for referencing column names in BioLang scripts or other tools.

Paste to Filter

Open a column's inline filter, then paste a list of values (one per line or comma-separated) into the filter input. The column is automatically filtered to show only rows matching the pasted values. Useful for filtering by a list of gene names, variant IDs, or sample identifiers from an external source.

Undo Toast

Press Ctrl+Z to undo the last action (cell edit, find & replace, column delete, sort reset). A brief toast notification appears confirming the undo. Multiple undo levels are supported — keep pressing Ctrl+Z to step back through the history.

Data Quality Badge

Each tab tooltip includes a data quality score, shown as a percentage badge. The score is composed of two metrics:

• Completeness % — percentage of non-empty cells across all columns
• Validity % — percentage of values that pass format-specific checks (e.g., valid chromosome names, positive coordinates, parseable numbers)

GZ Decompression

BioPeek transparently decompresses .gz files using the browser's native DecompressionStream API. Drop a .vcf.gz, .fastq.gz, .bed.gz, or any gzipped bioinformatics file and it is decompressed on the fly — no server needed. The decompressed content is parsed and displayed exactly like a regular file.

Chunked Preview for Large Files

Files larger than 5 MB are loaded using chunked preview. The first chunk is parsed and displayed immediately while the rest of the file continues loading in the background. A progress indicator shows loading status. Table navigation is available as soon as the first chunk is ready, so you can start exploring without waiting for the full file.

FASTQ QC Panel

FASTQ files display a dedicated quality control panel in the Stats view with:

• Read statistics — total reads, mean/median length, min/max length
• Q30% — percentage of bases with quality score ≥ 30
• Quality histogram — SVG bar chart of per-base quality distribution
• Per-position quality — box-plot style chart showing quality across read positions
• GC content distribution — per-read GC% histogram

FASTQ Quality Heatmap Bars

In the table view, FASTQ quality strings are rendered as colored heatmap bars. Each character in the quality string is mapped to a color: green for high quality (≥ Q30), amber for medium (Q20–Q29), and red for low (< Q20). This gives instant visual feedback on per-base quality without switching to the Stats view.

VCF Variant Density Chart

VCF files show a per-chromosome variant density chart in the Stats view. Each chromosome is displayed as a horizontal bar with variant count. The chart gives an immediate overview of variant distribution across the genome. Click a chromosome bar to filter the table to that chromosome.

VCF FILTER Pie Chart

VCF Stats view includes a donut chart showing the distribution of FILTER values (PASS vs. various filter flags). Hover over segments to see counts and percentages. Click a segment to filter the table to that FILTER value. Useful for quick assessment of variant call quality.

Strand Indicators

BED and GFF files display visual strand indicators in the strand column. Plus strand (+) is shown with a right-pointing arrow in green, minus strand (-) with a left-pointing arrow in rose, and unknown strand (.) with a dot in gray. Makes strand orientation immediately visible when scanning the table.

Copy as BioLang

Right-click any table view and select "Copy as BioLang" to generate BioLang pipe code that reproduces your current view. The generated code includes the file load, any active filters, sort order, and column selection. Paste it into the BioLang console or a .bl script to reproduce the analysis programmatically.

Copy as FASTA / Copy as BED

The cell context menu includes format-aware copy options. Right-click a sequence cell and select "Copy as FASTA" to copy it wrapped with a FASTA header. Right-click a row in a genomic file and select "Copy as BED" to copy the region as a BED line. Useful for quickly extracting data for use in other tools.

URL Loading with CORS Proxy Fallback

When loading a remote file via the ?url= parameter, BioPeek first attempts a direct fetch. If the request fails due to CORS restrictions, it automatically retries through a CORS proxy. A notification indicates when the proxy fallback is used. This allows loading files from servers that do not set CORS headers, such as many FTP mirrors and institutional repositories.

PostMessage File Receive

BioPeek listens for postMessage events from other browser contexts. The BioGist extension uses this to send detected file links directly to BioPeek for visualization. Other integrations can send file content or URLs via the window.postMessage API with the message type biopeek-open.

Inline Docs Hover Tooltips

In the BioLang console (view mode 4), hovering over builtin function names shows inline documentation tooltips with the function signature, description, and a usage example. This provides quick reference without leaving the console or switching to the docs.

⚙ Streaming Full-File Stats

For files larger than 50 MB (which are truncated to the first 50 MB for table display), a Compute full stats button appears in the Stats view. Clicking it streams through the entire file in 8 MB chunks without loading everything into memory.

A progress bar shows streaming progress. Stats update incrementally as each chunk is processed. The final result includes total row count, column statistics, and format-specific metrics for the complete file.

Streaming Stats for Large Files

For files larger than 50 MB, only the first 50 MB is loaded into the table view. To get accurate statistics for the entire file, click the Compute full stats button that appears in the Stats view.

• Streams the file in 8 MB chunks without loading the entire file into memory
• Uses Welford's online algorithm for exact mean, variance, and standard deviation
• Uses reservoir sampling (k=1000) for approximate median and percentiles
• Full exact counting for categorical value frequencies
• A progress bar shows streaming progress as each chunk is processed
• Stats update incrementally — you can see partial results while streaming continues