Search Results for "bioinformatics"
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Showing 404 open source projects for "bioinformatics"
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Volcano
A Cloud Native Batch System (Project under CNCF)
Volcano is a batch system built on Kubernetes. It provides a suite of mechanisms that are commonly required by many classes of batch & elastic workload including machine learning/deep learning, bioinformatics/genomics, and other "big data" applications. These types of applications typically run on generalized domain frameworks like TensorFlow, Spark, Ray, PyTorch, MPI, etc, which Volcano integrates with. Volcano builds upon a decade and a half of experience running a wide variety of high-performance workloads at scale using several systems and platforms, combined with best-of-breed ideas and practices from the open-source community. ... -
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing... -
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AlphaFold 3
AlphaFold 3 inference pipeline
...This repository provides the complete inference pipeline for running AlphaFold 3, though access to the model parameters is restricted and must be obtained directly from Google under specific terms of use. The system is designed for scientific research applications in structural biology, biochemistry, and bioinformatics, enabling accurate modeling of proteins, ligands, and covalent modifications. Users can perform local predictions via Docker containers, integrating AlphaFold 3’s inference process with provided JSON input configurations. The software includes flexible options for running both data preprocessing and GPU-accelerated inference, allowing users to adapt to available computational resources. -
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Codon
A high-performance, zero-overhead, extensible Python compiler
...The Codon framework is fully modular and extensible, allowing for the seamless integration of new modules, compiler optimizations, domain-specific languages and so on. We actively develop Codon extensions for a number of domains such as bioinformatics and quantitative finance. -
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nextflow
A DSL for data-driven computational pipelines
Nextflow is a powerful workflow orchestration tool designed for the development and execution of data-intensive pipelines, especially in the field of bioinformatics. It enables reproducible and portable workflows that can run seamlessly across different environments including local, HPC clusters, and cloud platforms. With support for containers and software package managers, Nextflow makes it easy to define complex data processes using a concise DSL and manage dependencies efficiently. -
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audioFlux
A library for audio and music analysis, feature extraction
A library for audio and music analysis, and feature extraction. Can be used for deep learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. audioflux is a deep learning tool library for audio and music analysis, feature extraction. It supports dozens of time-frequency analysis transformation methods and hundreds of corresponding time-domain and frequency-domain feature combinations. It can be provided to deep learning networks for training and is used to study various tasks in the audio field such as Classification, Separation, Music Information Retrieval(MIR) ASR, etc. -
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DGL
Python package built to ease deep learning on graph
...Scale to giant graphs via multi-GPU acceleration and distributed training infrastructure. DGL empowers a variety of domain-specific projects including DGL-KE for learning large-scale knowledge graph embeddings, DGL-LifeSci for bioinformatics and cheminformatics, and many others. We are keen to bringing graphs closer to deep learning researchers. We want to make it easy to implement graph neural networks model family. We also want to make the combination of graph based modules and tensor based modules (PyTorch or MXNet) as smooth as possible. DGL provides a powerful graph object that can reside on either CPU or GPU. ... -
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...Especially, it supports whole genome sequencing data even with low sequencing depth. If you use Lep-MAP3, please cite P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494. Please note Lep-Anchor for anchoring genomes with Lep-MAP3 linkage maps http://sourceforge.net/projects/lep-anchor
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Lep-Anchor
Linkage map guided genome anchoring
Lep-Anchor has been developed to efficiently anchor genomes into chromosomes by using all the information provided by Lep-MAP3 and the additional information provided by long reads and contig-contig alignments to link contigs and to collapse haplotypes. Lep-Anchor supports millions of markers over multiple maps. Pasi Rastas, Lep-Anchor: Automated construction of linkage map anchored haploid genomes, Bioinformatics, btz978, https://doi.org/10.1093/bioinformatics/btz978 -
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Armadillo
fast C++ library for linear algebra & scientific computing
* Fast C++ library for linear algebra (matrix maths) and scientific computing * Easy to use functions and syntax, deliberately similar to Matlab / Octave * Uses template meta-programming techniques to increase efficiency * Provides user-friendly wrappers for OpenBLAS, Intel MKL, LAPACK, ATLAS, ARPACK, SuperLU and FFTW libraries * Useful for machine learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. * Downloads: http://arma.sourceforge.net/download.html * Documentation: http://arma.sourceforge.net/docs.html * Bug reports: http://arma.sourceforge.net/faq.html * Git repo: https://gitlab.com/conradsnicta/armadillo-code -
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TomoJ
ImageJ plugin to perform Electron Tomography
...registration is described in: Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al -
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CpGtools
Python package to analyze DNA methylation data
CpGtools package provides a number of Python programs to annotate, QC, visualize, and analyze DNA methylation data generated from Illumina HumanMethylation450 BeadChip (450K) / MethylationEPIC BeadChip (850K) array or RRBS / WGBS. -
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Fastq-Fasta Converter
A bioinformatics tool that converts Fastq into Fasta
Fastq-Fasta Converter is a desktop application that converts Fastq files into Fasta files. -
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CpDB tutorial
Hands-on automatic annotation tutorial in Linux
This tutorial was conceived for a five hours course teaching automatic annotation to students with basic Linux OS concepts and some bioinformatics background. This is part of a book chapter available at the address https://doi.org/10.5772/23724. This is an alternative mirror for the site presented in the book chapter, a site no longer available. The parser's source code is available at sourceforge.net/projects/cpdb/. -
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com-hfg
java library for XML, HTML, or SVG generation + bioinformatics classes
The com.hfg (hairyfatguy.com) library is a collection of utility classes that make it easy to construct XML, HTML, XHTML, or SVG in an object-oriented way from within your Java application or webapp. It also contains other IO utilities and bioinformatics classes for phylogenetic trees, taxonomy, and multi-chain proteins. Requires JDK1.8. -
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CIERA
Crop Information Engine and Research Assistant
CIERA is a data management system for multi-crop breeding programs. It handles the genealogy, phenotypic and genotypic data of most modern breeding programs. It is distributed under the GNU General Public License, Version 3. ** This site is under construction, as of June 2024. *** -
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BioBytes PairSync
A Bioinformatics Tool for Basic Information Retrieval
This GUI app allows users to input biological sequences, either manually or by loading from a file. It supports DNA, RNA, and Protein sequences. Users can retrieve various information about the input sequence, such as nucleotide or amino acid frequency, GC content, reverse complement, transcription, translation, amino acid molecular weight, isoelectric point, and open reading frames. Users can save the output information to a text file and clear the output section for a clean slate.... -
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Bandicoot
fast C++ library for GPU linear algebra & scientific computing
* Fast GPU linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use * Provides high-level syntax and functionality deliberately similar to Matlab * Provides an API that is aiming to be compatible with Armadillo for easy transition between CPU and GPU linear algebra code * Useful for algorithm development directly in C++, or quick conversion of research code into production environments * Distributed under the permissive Apache 2.0 license, useful for both open-source and proprietary (closed-source) software * Can be used for machine learning, pattern recognition, computer vision, signal processing, bioinformatics, statistics, finance, etc * Downloads: http://coot.sourceforge.io/download.html * Documentation: http://coot.sourceforge.io/docs.html * Bug reports: http://coot.sourceforge.io/faq.html * Git repo: https://gitlab.com/conradsnicta/bandicoot-code -
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QUAST
Quality Assessment Tool for Genome Assemblies
...The tool also produces web-based reports condensing all information in one easy-to-navigate file. QUAST and its three follow-up papers (MetaQUAST, Icarus, QUAST-LG) papers were published in Bioinformatics; the last paper (WebQUAST) is out in Nucl Acid Research. -
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Despite the substantial progress facilitated by bioinformatics tool development, some of them are tailored for specific analytical objectives and code-based, and challenges arise when non-bioinformaticians users need to integrate the outputs of these specific tools into a personalized and appropriate pipeline for their research demands. To address this, we developed BioPipeline Creator, a user-friendly Java-based GUI for managing and customizing biological data pipelines according to end-user final demand.
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels of spectra, peptides and proteins, PANDA works out a few quantitative filters and new scores for quantification confidence. Third, PANDA is designed for processing proteomics big data in parallel. -
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DataPrep
Python-based data preprocessing tool
DataPrep v0.2 is a Tkinter-based GUI application/tool designed to assist users in data preprocessing, multicollinearity removal, and feature selection for a wide range of applications in Cheminformatics, Bioinformatics, Data Analysis, Feature Selection, Molecular Modeling, Machine Learning, and Quantitative-structure-property relationship (QSPR) studies. It includes functionality to load, process, and save datasets with support for different preprocessing & multicollinearity removal strategies with customizable parameter setting options. -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Please, do not hesitate to contact us if you need help. https://sites.google.com/view/hsa23/ Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. ... -
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
...The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
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AngClust
AngClust: Angle-based feature clustering for time series
Citation: Aimin Li, Siqi Xiong, Junhuai Li, Saurav Mallik, Yajun Liu, Rong Fei, Hongfang Zhou, Guangming Liu. AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles. January 2022. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. DOI: 10.1109/TCBB.2022.3192306 Full text: https://ieeexplore.ieee.org/document/9833353/ https://pubmed.ncbi.nlm.nih.gov/35853049/ Highlights * We proposed a novel clustering algorithm based on angular features for short-term gene expression profiles. * We defined three indicators to identify significant clusters: (i) the fluctuation degree of expression levels, (ii) homogeneity, and (iii) the degree of clustering while the clusters are functionally significant...
