Search Results for "collection"
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Showing 84 open source projects for "collection"
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QUANTUM SALIS
Statistical algorithms for life sciences
Collection of algorithms for computational statistics in life sciences -
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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PUMA Repository
Pascal Units for Medical Applications
The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers. -
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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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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. ... -
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JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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EasierMGF
Converts RAW Thermo Files into MGF files
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/easiermgf3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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OmssaGUI
GUI front-end for OMSSA
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/omssagui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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SequestGUI
GUI front-end to sequest.exe
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/sequestgui/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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FastaTools
Performs several operations to Fasta protein databases
...For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/fastatools/code/ci/default/tree/README.md Or you can download the Documentation an Tutorial PDF file in the Files section: https://sourceforge.net/projects/fastatools.lp-csic-uab.p/files/FastaTools%20Documentation%20and%20Tutorials.pdf - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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LymPHOS2
LymPHOS2 Web-App
...DOI: 10.1021/pr800500r - Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. Proteomics 2014, 20, 2275-2279. DOI: 10.1002/pmic.20140012 -
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epidaurus
tumor epigenetic database
Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets. -
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An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).
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BioUtils Perl Library
A collection of Perl modules for handling fasta/q sequences and files.
WARNING: BioUtils has been migrated to Github (Nov 2017). For the most up-to-date versions and info please visit: https://github.com/islandhopper81/BioUtils BioUtils are a collection of Perl modules for DNA sequence analysis in bioinformatics. BioUtils is a significantly faster and more memory efficient alternative to BioPerl. However, it's functionality is currently limited to the features listed below. -
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WrapImaJ
Multi-platform API for Image Processing systems in Life Sciences
WrapImaJ purposes to be a multi-platform wrapper for different Image Processing systems for: - using the Java programming language. The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. In it's current form, it only wraps basic functionalities of ImageJ. ... -
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EXCAVATOR2tool
Enhanced tool for detecting CNVs from whole-exome sequencing data
...We recently published on BMC Genomics a novel software package, named XCAVATOR, for the identification of CNVs/CNAs from short and long reads whole-genome sequencing experiments (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4137-0). XCAVATOR is freely available at http://sourceforge.net/projects/xcavator/. EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads. EXCAVATOR2 can be effectively employed for the identification of CNVs in small as well as large-scale re-sequencing population and cancer studies. ... -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. -
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CNVision
CNV prediction from Illumina genotyping data
...The script is optimized to work in a UNIX-based environment; it should work in Windows, however running the PennCNV component gives errors with the newer versions of PennCNV. CNVision was written to analyze data for the Simons Simplex Collection (SSC) autism data. A fill description of methods are given in the following paper which can be used to reference CNVision: http://www.ncbi.nlm.nih.gov/pubmed/21658581 -
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memesa-tools
A collection of tools used in the enumeration of solution spaces
This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function. -
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AMOS
AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. -
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CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems.
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SyntheticWSI
Tools to generate and visualize artificial whole slide images
Java 8+ required. Collection of tools to help generate artificial Whole Slide Images (WSIs). A WSI is stored as a ZIP archive of JPG tiles, and this software contains a tool to visualize this format. SVS files can be used directly for texture extraction (thanks to the included Bio-Formats library). Main source files in package fr.unistra.wsi.synthetic. -
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Pipeline Builder for NGS tools
Scripting tool for automatize and managing complex NGS analysis
Handling with NGS tool configuration files is a real challenge for modern biologists and biotechnologist. To increase productivity, specificity and enhance the data processing, this tool provides a collection of commands already structured, leading the user in building the correct pipeline for the data he has to analyse. Pipeline Builder is a scripting tool for managing complex NGS analysis pipelines. It helps the user in composing NGS tool commands and composing his own analysis pipeline. It allows for data independent reproducible analysis creating protected environment which separates data from results through variable exportation. ... -
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Zoorbar 3.0
Zoorbar 3.0, software to manage and digitize zoological collection
Zoorbar 3.0 is the updated version of a software application based on MS-Access, designed to manage and digitize zoological collections. Find credits and further information about Zoorbar 3.0 on its website: http://www.gbif.es/zoorbar/zoorbar.php.
