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Showing 38 open source projects for "get"
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AlphaGenome
Programmatic access to the AlphaGenome model
The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can... -
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BioEmu
Inference code for scalable emulation of protein equilibrium ensembles
Biomolecular Emulator (BioEmu for short) is a model that samples from the approximated equilibrium distribution of structures for a protein monomer, given its amino acid sequence. By default, unphysical structures (steric clashes or chain discontinuities) will be filtered out, so you will typically get fewer samples in the output than requested. The difference can be very large if your protein has large disordered regions, which are very likely to produce clashes. BioEmu outputs structures in backbone frame representation. To reconstruct the side-chains, several tools are available. As an example, we interface with HPacker to conduct side-chain reconstruction and also provide basic tooling for running a short molecular dynamics (MD) equilibration. -
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code" button. View a 3D structure in iCn3D, input a PDB ID, and click "Load". You can also click the "File" menu to "Open File" or input other IDs. You can open a browser in your Virtual Reality (VR) headset and view a 3D structure in iCn3D. Then click the button "Enter VR" at the bottom center of your browser to enter the VR view. ... -
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ViReMa
Viral Recombination Mapper
...Feb 2014 - Our paper (Open Access) is available at Nucleic Acids Research: "Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data" http://nar.oxfordjournals.org/content/42/2/e11 This is an on-going project and updates will be regularly posted. Please get in touch with any questions, problems or suggestions. -
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
...LINUX, MAC OR WINDOWS SPECIFIED FOLDER) TO ALLOW THE PROGRAM TO FIND THE PREDESIGNED DATA. * UPDATE NOTE: -> Sep-1-2020: add an update for Ubuntu-20.04. You will need Boost library installed (sudo apt-get install libboost-all-dev) -> Mar-7-2018: revise header terms in the output file -
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006).
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project... -
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CSBB-v2.1 [CSBB-v3.0 is now available]
Computational Suite For Bioinformaticians and Biologists
...CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 17 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc. -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
...CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX. Currently CSBB provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. ... -
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CSBB-v2.0
Computational Suite for Bioinformaticians and Biologists
...CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 16 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc. -
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ConvertMAS
ConvertMAS converts Chemical File Formats mol, mol2 and sdf.
...It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available for conversion of Chemical file formats; but ConvertMAS mainly works on mol, mol2 and sdf effectively. -
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Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
...Shoal Shell Project needs grownup I'm just a student in the university, and the shoal shell just in its begining, if you have any idea about shoal, please contact me from xie.guigang@gmail.com. The Shoal shell needs your professional advice. Try get some help (if you want build the shoal library by yourself): https://sourceforge.net/p/shoal/wiki/Shoal%20Developer%20Guide/ -
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iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS. Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class. See the change log for full details.
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This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
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NIKS
NIKS (Needle in a K-stack) - detection of mutations in NGS data
To get access to the code, please check it out with svn as described in the code section. -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a... -
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NISA
Image Stack Analyzer
OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state. -
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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tinyMOBY
Semantically enriched WSDL 2.0 descriptors for BioMoby services
...The library interacts with BioMoby Central Registry and may automatically generate appropriate WSDL 2.0 descriptors using BioMoby service identifiers (LSIDs). Generated WSDL 2.0 descriptors may be used then to get a complete definition of the services in MobyCore model, that facilitates further services execution. -
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NGS can product a pair of reads which come from one original DNA fragment. If the internal gap can be correctly filled, we will get the full length sequence of original DNA fragment.
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SBEToolbox
Systems Biology and Evolution Toolbox (SBEToolbox).
SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven UI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne) etc... ******************************************************************************************************************************** PROJECT... -
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SeqWare has moved to GitHub, see https://github.com/SeqWare SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
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SPA - SNP based pathway analysis
SNP based pathway analysis
Name: SPA Full name: SNP based pathway analysis Maintainer: jiangyongshuai@gmail.com liuguiyou1981@163.com Language: R package Description: SPA is an R package which can identify disease or phenotype related pathways. Input rs# and GWAS test p-values, you can get the related pathways. -
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FluxY
FluxY – a processing tool set for stable isotope label MS data
FluxY is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data used for metabolic flux analysis. To get started simply download and unzip the FluxY.zip file and follow the getting started document in the Instructions folder.
