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A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats

Python 65 10 Updated May 22, 2021

🗻 Fuji plot—a circos representation of multiple GWAS results— 🗻

R 81 19 Updated Feb 14, 2024

Modelling of MIAPPE

8 3 Updated Jan 5, 2023

Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.

C 53 13 Updated Nov 9, 2024

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…

C++ 276 50 Updated May 9, 2024

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Scala 1,016 311 Updated Feb 12, 2025

Java library for nanopublications based on RDF4J

Java 25 11 Updated Feb 13, 2025

Hagfish - assess an assembly through creative use of coverage plots

Python 36 4 Updated Aug 9, 2012

VariantToolChest (VTC) is intended to be a powerful tool chest to analyze VCF files. I encourage anyone to contribute their tools and help improve existing tools. VTC currently provides two powerfu…

Java 25 9 Updated Apr 8, 2016

OmicsFusion is a web application which can perform univariate regression and a number of modern regression techniques and then ranks the predictors according to an importance criterion (mean rank o…

Java 1 Updated Apr 5, 2019

Tools for working with second gen assemblies, fasta sequences, etc

Perl 93 36 Updated Sep 8, 2016

Repetitive motif detection by Assembly of Repetitive K-mers. RepARK is free for academic and non-profit use. By downloading you agree with the FLI-LICENSE included in the package.

Perl 16 5 Updated Sep 16, 2024

A professional front-end template for building fast, robust, and adaptable web apps or sites.

JavaScript 56,796 12,267 Updated Feb 5, 2025

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

C++ 807 265 Updated Feb 25, 2025

Project directory for the analysis of ancient tomato DNA

HTML 1 1 Updated Mar 23, 2018

Java utilities for Bioinformatics

Java 493 133 Updated Feb 26, 2025

RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.

Python 2,215 569 Updated Feb 24, 2025

Subset of the kent source libraries (perhaps out of date) that are easily built and installed on OSX and Linux. These libraries provide usefull utilities for bioinformatics programming in C. This m…

C 13 3 Updated Oct 30, 2012

RStudio is an integrated development environment (IDE) for R

Java 4,759 1,110 Updated Feb 27, 2025

Reference-based compression of SRA data

Java 36 5 Updated Mar 26, 2013

Scripts for design of PCR-based Marker Assays from DNA sequence variant data, plus Galaxy xml files

Python 7 10 Updated Mar 22, 2017

Java library to automatically link a chebi compound/identifier to a metabolic pathway or genes from the tomato genome.

Java 3 Updated Nov 14, 2015

Personal github page

2 Updated Jun 13, 2012

Phenotype Database

Groovy 10 8 Updated Sep 15, 2020

LINKED DATA QUALITY REPORTS

HTML 41 7 Updated May 20, 2022

Breakpointer is a fast algorithm to locate breakpoints of structural variants from single-end reads produced by next-generation sequencing.

C 10 2 Updated May 2, 2014

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

Java 294 224 Updated Aug 22, 2018
C++ 89 30 Updated Jan 11, 2022

An ontology database for crops' traits with their variables

CSS 20 8 Updated Jun 17, 2024

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

Python 257 157 Updated Dec 19, 2023
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