Genomics Libraries - Page 3

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

C++ 420Updated: 11 mo ago License: Weak Copyleft (LGPL-3.0)

Plot structural variant signals from many BAMs and CRAMs

Python 418Updated: 11 mo ago License: Permissive (MIT)

Source repository for fiat tokens on the CENTRE network.

JavaScript 418Updated: 10 mo ago License: Permissive (MIT)

Java utilities for Bioinformatics

Java 416Updated: 11 mo ago License: Proprietary (Proprietary)

SmartBugs: A Framework to Analyze Ethereum Smart Contracts

Python 412Updated: 10 mo ago License: Permissive (Apache-2.0)

Structural variation caller using third generation sequencing

Python 410Updated: 1 y ago License: Permissive (MIT)

Copy number variant detection from targeted DNA sequencing

Python 406Updated: 11 mo ago License: Proprietary (Proprietary)

A comprehensive library for computational molecular biology

Python 405Updated: 11 mo ago License: Permissive (BSD-3-Clause)

SeqAn's official repository.

C++ 395Updated: 3 y ago License: Proprietary (Proprietary)

Official repository for the QIIME 2 framework.

Python 394Updated: 11 mo ago License: Permissive (BSD-3-Clause)

COBRApy is a package for constraint-based modeling of metabolic networks.

Jupyter Notebook 394Updated: 1 y ago License: Strong Copyleft (GPL-2.0)

Gene Set Enrichment Analysis in Python

Python 392Updated: 12 mo ago License: Permissive (BSD-3-Clause)

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

Python 389Updated: 11 mo ago License: Strong Copyleft (GPL-3.0)

Deep generative modeling for single-cell omics data

Python 388Updated: 4 y ago License: Permissive (MIT)

Accurate sample inference from amplicon data with single nucleotide resolution

R 388Updated: 11 mo ago License: Weak Copyleft (LGPL-3.0)

A fast multi-threaded k-mer counter

C++ 388Updated: 10 mo ago License: Proprietary (Proprietary)

https://www.sc-best-practices.org

Jupyter Notebook 386Updated: 10 mo ago License: Proprietary (Proprietary)

Efficient pythonic random access to fasta subsequences

Python 384Updated: 1 y ago License: Proprietary (Proprietary)

:scissors: :zap: Rapid haploid variant calling and core genome alignment

Perl 384Updated: 10 mo ago License: Strong Copyleft (GPL-2.0)

C/C++ to assembly visualizer

HTML 380Updated: 3 y ago License: No License (No License)

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

Perl 374Updated: 11 mo ago License: Permissive (Apache-2.0)

An analysis and visualization platform for 'omics data

Python 369Updated: 11 mo ago License: Strong Copyleft (GPL-3.0)

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Perl 368Updated: 1 y ago License: Strong Copyleft (GPL-3.0)

Quickly search, compare, and analyze genomic and metagenomic data sets.

Python 368Updated: 10 mo ago License: Proprietary (Proprietary)

A list of scRNA-seq analysis tools

R 362Updated: 1 y ago License: Permissive (MIT)

Mummer alignment tool

C++ 357Updated: 10 mo ago License: Weak Copyleft (Artistic-2.0)

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

R 356Updated: 1 y ago License: Permissive (MIT)

Prodigal Gene Prediction Software

C 354Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)

NicheNet: predict active ligand-target links between interacting cells

R 353Updated: 10 mo ago License: No License (No License)

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

Python 352Updated: 3 y ago License: Strong Copyleft (GPL-3.0)

Haplotype VCF comparison tools

C++ 349Updated: 11 mo ago License: Proprietary (Proprietary)

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

C++ 347Updated: 11 mo ago License: Permissive (BSD-3-Clause)

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

Python 345Updated: 10 mo ago License: Permissive (BSD-3-Clause)

Data and analysis for NA12878 genome on nanopore

Python 344Updated: 1 y ago License: Proprietary (Proprietary)

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

C++ 344Updated: 1 y ago License: Strong Copyleft (GPL-3.0)

Performant Pythonic GenomicRanges

Python 343Updated: 11 mo ago License: Permissive (MIT)

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

C++ 342Updated: 1 y ago License: Permissive (MIT)

Structural variant and indel caller for mapped sequencing data

C++ 342Updated: 1 y ago License: Strong Copyleft (GPL-3.0)

Performant Pythonic GenomicRanges

Python 340Updated: 12 mo ago License: Permissive (MIT)

Graph-based alignment (Hierarchical Graph FM index)

C++ 339Updated: 2 y ago License: Strong Copyleft (GPL-3.0)

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Python 337Updated: 11 mo ago License: Strong Copyleft (GPL-3.0)

Tools for fast and flexible genome assembly scaffolding and improvement

Python 336Updated: 11 mo ago License: Permissive (MIT)

RNA Velocity generalized through dynamical modeling

Python 334Updated: 10 mo ago License: Permissive (BSD-3-Clause)

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

C++ 334Updated: 11 mo ago License: Proprietary (Proprietary)

Python functions for reading kaldi data formats. Useful for rapid prototyping with python.

Python 332Updated: 3 y ago License: Permissive (Apache-2.0)

Customizable workflows based on snakemake and python for the analysis of NGS data

Python 327Updated: 10 mo ago License: Permissive (MIT)

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Shell 327Updated: 11 mo ago License: Permissive (MIT)

Proof-of-concept seq-to-graph mapper and graph generator

C 326Updated: 10 mo ago License: Permissive (MIT)

UICollectionView layout for presenting of the overlapping cells.

Swift 326Updated: 3 y ago License: Permissive (MIT)

genes and genomes at your fingertips

Python 324Updated: 11 mo ago License: Permissive (MIT)