Search Results for "bioinformatics"
Sort By:
Showing 403 open source projects for "bioinformatics"
View related business solutions-
Simple, Secure Domain RegistrationRegister or renew your domain and pay only what we pay. No markups, hidden fees, or surprise add-ons. Choose from over 400 TLDs (.com, .ai, .dev). Every domain is integrated with Cloudflare's industry-leading DNS, CDN, and free SSL to make your site faster and more secure. Simple, secure, at-cost domain registration.
-
The All-in-One Commerce Platform for Businesses - ShopifyShopify is a leading all-in-one commerce platform that enables businesses to start, build, and grow their online and physical stores. It offers tools to create customized websites, manage inventory, process payments, and sell across multiple channels including online, in-person, wholesale, and global markets. The platform includes integrated marketing tools, analytics, and customer engagement features to help merchants reach and retain customers. Shopify supports thousands of third-party apps and offers developer-friendly APIs for custom solutions. With world-class checkout technology, Shopify powers over 150 million high-intent shoppers worldwide. Its reliable, scalable infrastructure ensures fast performance and seamless operations at any business size.
-
1
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... -
2
Codon
A high-performance, zero-overhead, extensible Python compiler
... for a number of domains such as bioinformatics and quantitative finance. -
3
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. -
4
AlphaFold 3
AlphaFold 3 inference pipeline
AlphaFold 3, developed by Google DeepMind, is an advanced deep learning system for predicting biomolecular structures and interactions with exceptional accuracy. 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... -
Gen AI apps are built with MongoDB AtlasMongoDB Atlas provides built-in vector search and a flexible document model so developers can build, scale, and run gen AI apps without stitching together multiple databases. From LLM integration to semantic search, Atlas simplifies your AI architecture—and it’s free to get started.
-
5
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... -
6
DGL
Python package built to ease deep learning on graph
Build your models with PyTorch, TensorFlow or Apache MXNet. Fast and memory-efficient message passing primitives for training Graph Neural Networks. 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... -
7
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... -
8
kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
..., unassembled reads. Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
9
Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families. 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...
-
Level Up Your Cyber Defense with External Threat ManagementMove beyond alerts. Gain full visibility, context, and control over your external attack surface to stay ahead of every threat.
-
10
QUAST
Quality Assessment Tool for Genome Assemblies
... analysis results in summary tables (in plain text, tab-separated, and LaTeX formats) and colorful plots. 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. -
11
TomoJ
ImageJ plugin to perform Electron Tomography
..., 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 -
12
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 -
13
... websites: https://tangsoftwarelab.shinyapps.io/synergyfinder/ Bioconductor R package: https://www.bioconductor.org/packages/release/bioc/html/synergyfinder.html Citation: Zheng, S.; Wang, W.; Aldahdooh, J.; Malyutina, A.; Shadbahr, T.; Tanoli Z; Pessia, A.; Tang, J. SynergyFinder Plus: Toward Better Interpretation and Annotation of Drug Combination Screening Datasets. Genomics, Proteomics & Bioinformatics 2022, 20, 587-596 https://doi.org/10.1016/j.gpb.2022.01.004
-
14
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... -
15
Gemi
PCR primers / probes design from multiple & degenerate sequences
Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. 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... -
16
Bandicoot
fast C++ library for GPU linear algebra & scientific computing
... 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 -
17
123VCF
An Intuitive and Efficient Tool for VCF file filtration
... Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
18
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...
-
19
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. -
20
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/. -
21
CpDB
Relational database schema and tools for bacterial genome annotation
This software allows us to create a relational database in PostgreSQL hosting full bacterial genomes. Besides the database, there is software, like a parser, to convert EMBL or GBK files to the CpDB relational schema. Once in the CpDB, one can extract unlimited reports from bacterial genomes using SQL. This software is part of the Ph.D. in Bioinformatics from Anderson Santos (https://orcid.org/0000-0003-3418-0823) developed under the Corynebacterium pseudotuberculosis (Cp) pangenome project... -
22
OmicsSuite
OmicsSuite: a suite for multi-omics analysis and visualization.
OmicsSuite (https://github.com/OmicsSuite/, https://omicssuite.github.io), original name BioSciTools, a desktop program developed based on Java 11, aims to make new exploration and contribution to the development of bioinformatics, and realize data analysis and visualization in the fields of sequence analysis, multimomics (transcriptomics, genomics, protein omics, metabonomics, single cell), microbiology, clinical, etc. The program inherits the excellent interactive components, perfect analysis... -
23
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. -
24
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. *** -
25
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....
