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Pyranges v1: a Python framework for ultrafast sequence interval operations

Stovner, E. B.; Tico, M.; Munoz del Campo, E.; Pallares-Albanell, J.; Chawla, K.; Saetrom, P.; Mariotti, M.

2025-12-12 bioinformatics
10.64898/2025.12.11.693639 bioRxiv
Show abstract

Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice intervals), enabling the intuitive development of efficient pipelines for diverse sequence data, including gene annotations, mapped reads, and protein domains. Pyranges is faster, consumes less memory, and offers more functionalities than alternative tools including BEDTools, emerging as an innovative one-stop shop for omics analysis.

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
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7.2%
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4
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Top 1%
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8
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Top 1%
4.0%
9
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○ 457 papers in training set
Top 3%
2.4%
10
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Top 5%
1.7%
11
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12
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13
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14
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15
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16
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● 1863 papers in training set
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17
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○ 286 papers in training set
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18
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Top 9%
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19
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○ 3612 papers in training set
Top 77%
0.6%
20
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○ 993 papers in training set
Top 36%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.