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    43 repositories

    • prymer

      Public
      Python Primer Design Library
      bioinformaticsgenomicsprimer-design
      Python
      •
      MIT License
      •0•8•33•3•Updated Nov 19, 2024Nov 19, 2024

    • fgpyo

      Public
      Quality of life improvements for Bioinformatics in Python.
      bioinformaticsgenomicspython
      Python
      •
      Other
      •3•27•28•8•Updated Nov 14, 2024Nov 14, 2024

    • Sniffles

      Public
      Structural variation caller using third generation sequencing
      Python
      •
      Other
      •95•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • fgsv

      Public
      Tools to gather evidence for structural variation via breakpoint detection.
      bioinformaticsbreakpointstructural
      Scala
      •
      MIT License
      •1•19•9•1•Updated Nov 1, 2024Nov 1, 2024

    • fgbio

      Public
      Tools for working with genomic and high throughput sequencing data.
      genomicsngsumianalyzing-genomic-datafgbiomolecular-indexesbioinformaticsscala
      Scala
      •
      MIT License
      •67•315•96•34•Updated Nov 1, 2024Nov 1, 2024

    • regtools

      Public
      Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
      C++
      •
      MIT License
      •26•0•0•5•Updated Oct 31, 2024Oct 31, 2024

    • sopt

      Public
      An argument parsing library for Scala
      scalaargument-parsing
      Scala
      •
      MIT License
      •0•10•4•2•Updated Oct 4, 2024Oct 4, 2024

    • commons

      Public
      Common scala utilities
      Scala
      •
      MIT License
      •3•4•10•2•Updated Oct 4, 2024Oct 4, 2024

    • pooled-writer

      Public
      A pooled writer and compressor library in Rust.
      bioinformaticscompressionrust
      Rust
      •
      MIT License
      •0•4•0•0•Updated Oct 4, 2024Oct 4, 2024

    • guide-counter

      Public
      A better, faster way to count guides in CRISPR screens.
      bioinformaticsgenomicscrispr
      Rust
      •
      MIT License
      •3•28•8•1•Updated Oct 4, 2024Oct 4, 2024

    • read-structure

      Public
      read structures in rust
      Rust
      •
      MIT License
      •3•3•0•0•Updated Oct 4, 2024Oct 4, 2024

    • stitch

      Public
      Stitch is a toolkit for analysis of chimeric reads in sequencing data
      Rust
      •
      MIT License
      •3•9•14•1•Updated Oct 4, 2024Oct 4, 2024

    • fqgrep

      Public
      Grep for FASTQ files
      rustbioinformaticsgenomicsfastq
      Rust
      •
      MIT License
      •4•93•6•5•Updated Oct 4, 2024Oct 4, 2024

    • python-snakemake-template

      Public
      A template repository for Snakemake pipepline(s) and a python command-line toolkit.
      Python
      •
      MIT License
      •0•27•6•12•Updated Oct 4, 2024Oct 4, 2024

    • fgprimer

      Public
      APIs and wrappers for performing PCR primer design related tasks
      Scala
      •
      MIT License
      •1•0•5•3•Updated Oct 4, 2024Oct 4, 2024

    • pybedlite

      Public
      Lightweight Python interfaces for reading, writing, and querying Genomic Regions (BED)
      bioinformaticsgenomicsbed-filespython
      Python
      •
      Other
      •0•12•1•1•Updated Oct 4, 2024Oct 4, 2024

    • .github

      Public
      MIT License
      •0•1•0•0•Updated Oct 4, 2024Oct 4, 2024

    • bwa-aln-interactive

      Public
      BWA aln interactive: Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
      C
      •
      GNU General Public License v3.0
      •0•0•4•0•Updated Sep 20, 2024Sep 20, 2024

    • betabinom

      Public
      Maintained fork of `countdata`
      C
      •
      Other
      •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • leafcutter

      Public
      Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
      R
      •
      Apache License 2.0
      •115•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • fqtk

      Public
      Fast FASTQ sample demultiplexing in Rust.
      bioinformaticsgenomicsrust
      Rust
      •
      MIT License
      •1•57•5•6•Updated Aug 19, 2024Aug 19, 2024

    • fgoxide

      Public
      Quality of life improvements in Rust.
      Rust
      •
      MIT License
      •3•4•2•4•Updated Aug 19, 2024Aug 19, 2024

    • bamsurgeon

      Public
      tools for adding mutations to existing .bam files, used for testing mutation callers
      Python
      •
      MIT License
      •86•0•0•0•Updated Jul 17, 2024Jul 17, 2024

    • pyfgaws

      Public
      Python tools and APIs for working with AWS
      pythonawsbioinformaticsaws-batchaws-logs
      Python
      •
      MIT License
      •0•9•7•1•Updated Jun 20, 2024Jun 20, 2024

    • setup-latch

      Public
      MIT License
      •1•5•5•0•Updated May 20, 2024May 20, 2024

    • scala-mill-template

      Public
      A template repo for a Scala project with the build tool Mill
      Scala
      •
      MIT License
      •1•0•0•0•Updated May 20, 2024May 20, 2024

    • nf-dotenv

      Public
      Automatically source dotenv files into your Nextflow scope
      dotenvnextflow
      Groovy
      •
      Other
      •0•7•1•1•Updated Mar 5, 2024Mar 5, 2024

    • latch-snakemake-examples

      Public
      Python
      •1•0•0•0•Updated May 31, 2023May 31, 2023

    • nh13-testing-1

      Public
      0•0•0•0•Updated May 16, 2023May 16, 2023

    • nf-core-demultiplex

      Public
      Demultiplexing pipeline for sequencing data
      Nextflow
      •
      MIT License
      •38•0•0•1•Updated Mar 15, 2023Mar 15, 2023