Python for Command Line Oneliners
☆19Jan 5, 2015Updated 11 years ago
Alternatives and similar repositories for pype
Users that are interested in pype are comparing it to the libraries listed below
Sorting:
- 🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies☆17Jan 23, 2023Updated 3 years ago
- Lab notebook for people who like the command line.☆11Mar 6, 2026Updated 2 weeks ago
- Sweep-line algorithm for genomic features. Detect overlaps on large files w/ minimal memory.☆10Sep 13, 2011Updated 14 years ago
- Explore and analyze biological sequence data☆17Aug 1, 2024Updated last year
- Library for visualising genomic features in Python.☆15May 12, 2017Updated 8 years ago
- python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.☆15Feb 13, 2018Updated 8 years ago
- Bedfile perturbation tool☆17Mar 6, 2026Updated 2 weeks ago
- Code for performing PCA followed by CCA☆18Dec 2, 2018Updated 7 years ago
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 8 years ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆21Oct 20, 2023Updated 2 years ago
- Ultrafast interval trees from the kernel. Deprecated in favor of the NCLS.☆26Apr 8, 2019Updated 6 years ago
- ☆22Oct 6, 2023Updated 2 years ago
- Index and query k-mer matrices in BGZF☆12Apr 30, 2018Updated 7 years ago
- Percentile-normalization method for correcting batch effects in case-control studies☆12Oct 26, 2019Updated 6 years ago
- Anno is a variant annotation tool☆24May 18, 2016Updated 9 years ago
- Single-pass probabilistic duplicate marking of alignments with a Bloom filter.☆24Aug 7, 2023Updated 2 years ago
- A file watcher written in Rust☆11Dec 1, 2024Updated last year
- Bam to Pandas DataFrame, quickly☆13May 10, 2025Updated 10 months ago
- a cythonized, extended version of the interval search tree in bx☆30Jun 4, 2019Updated 6 years ago
- LAAVA: Long-read AAV Analysis☆13Dec 9, 2025Updated 3 months ago
- Python-based UCSC genome browser snapshot-taker and gallery-maker☆12May 21, 2024Updated last year
- A thorough, straightforward, un-intimidating introduction to Gaussian processes in NumPy.☆16Jun 12, 2018Updated 7 years ago
- GESTALT processing pipeline for barcodes captured with single-cell RNA sequencing☆13Jan 26, 2020Updated 6 years ago
- 📊 A working, maintained copy of ggpy☆31Jul 11, 2019Updated 6 years ago
- A small, auxiliary index to massively improve parallel fastq parsing☆31Mar 6, 2026Updated 2 weeks ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.☆18Jan 16, 2026Updated 2 months ago
- Robust individual and aggregate checksums for nucleotide sequences☆17Mar 3, 2026Updated 2 weeks ago
- Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang☆31Apr 20, 2020Updated 5 years ago
- A comprehensive and intelligent clinical phasing tool☆14Dec 3, 2022Updated 3 years ago
- ☆27Dec 22, 2025Updated 2 months ago
- Python bindings to minimap2☆16Sep 18, 2017Updated 8 years ago
- Benchmark structural variant calls against a reference set☆18Jan 26, 2026Updated last month
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated 3 months ago
- drunk on perbase pileups and lua expressions☆19Nov 15, 2025Updated 4 months ago
- K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data☆61Aug 30, 2022Updated 3 years ago
- Quality control methods for human genomic variants.☆61Sep 1, 2022Updated 3 years ago
- zsh plugin to list up EC2 instances and ssh login the instances.☆11Apr 10, 2018Updated 7 years ago
- Transfer HiFi read mappings from their own assembly contigs to a standard reference☆38Dec 30, 2025Updated 2 months ago