Search Results for "common"
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Showing 61 open source projects for "common"
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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MView
Extract and reformat a sequence database search or multiple alignment
.... ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). Found a bug? Please open an issue on the MView issue tracker at https://github.com/desmid/mview/issues or send an email to biomview@gmail.com. -
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the... -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and makes extensive use of Numpy/Scipy. You can use any supported toolkit united under common API (for reference see Pybel or Cinfony). All methods and software based on Pybel/Cinfony should be drop-in compatible with ODDT toolkits. In contrast to its predecessors, which were aimed to have minimalistic API, ODDT introduces extended methods and additional handles. These extensions allow to use of toolkits at all its grace and some features may be backported from others to introduce missing functionalities. ... -
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The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.
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SMSD
SMSD is a Java based software library for calculating MCS.
SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure). -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2...
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Niche Analyst (NicheA) was developed based on the BAM framework which allows users to create virtual spaces and virtual species, and to analyze ecological niches in both multivariate environmental and geographic spaces, linking views of the niche in the two spaces. The unique functionality in NicheA, not available in other software programs, is estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological...
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. -
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...More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform these common tasks. RUbioSeq+ is free and includes all the core functionalities implemented in the original release of RUbioSeq (v3.2.1) but, also, outperforms and expands RUbioSeq capabilities supporting the parallelized analysis of full genomes in computing farms. RUbioSeq+ also incorporates a new GUI designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together.
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures relying on both, sequence dependent mismatch patterns and RT arrests. Common alignment viewers lack in specialized functionality, such as filtering, tailored visualization, differential analysis and export. Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer was developed in response to the demand for a powerful inspection tool, running on all 3 OSes. ... -
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Projects and applications developed from the lab of Yuval Kluger at the Pathology department at Yale
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BioC
We describe a simple XML format to share text documents and annotation
... - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining. -
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Acacia
A generic biodiversity database management system
An interactive data entry, querying, and editing system based on a generic conceptual schema for taxonomic databases. It combines the automated use of scientific names and synonyms in a species checklist with online access to geographical data and common knowledge data (morphological descriptors, genomics, ecology, vernacular names, economic uses, structured notes and conservation status) about the species. All these data can be cross-indexed to a citation list. The design and standard permits rapid customization to suit any taxonomic group. -
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Sequencia
Protein Primary Sequnece Analysis
...Sequence Name, Sequence Length, Absorbance, Net charge, Iso electric charge, Amino acid composition, Amino acid classification, Aliphatic Index, Instability Index, Average Hydropathy etc are the Primary Sequence Analysis related Attributes for which this Tool exist. This work includes all the Physiochemical Properties- related to Primary Sequence Analysis under a common platform. JAVA, BIOJAVA were used under Platform Independent architecture. The Tool includes Properties of being offline where result can be stored in Text Format, here we can paste more than one sequence and also upload FASTA file to compute Parameters. -
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BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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HaploView is a Java based tool for use by biologists in the study of genetic haplotype data. It provides a quick, easy interface to many common tasks involved in such analyses. Please go to the homepage below for the latest version!
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pipasic
pipasic: Protein Abundance Correction in Metaproteomic Data
...pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor. -
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fitGCP
Fitting genome coverage distributions with mixture models
...fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Please find the accompanying paper here: http://dx.doi.org/10.1093/bioinformatics/btt147 -
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. ... -
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StatAlign
An extendable statistical multiple alignment tool.
...Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single (probably suboptimal) alignment and bias towards the guide tree upon which the alignment relies. The models behind the analysis permit the comparison of evolutionarily distant sequences: the TKF92 insertion-deletion model can be coupled to an arbitrary substitution model. ... -
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
...To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of heterozygosity (LOH) events in Candida albicans, the most common human fungal pathogen, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains. The YMAP pipeline automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other categories of data and other pathogen species with small genomes. -
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miRStat
identification of common sets of microRNAs for groups of genes
miRStat enables identification of regulatory microRNA targeting several genes in a custom gene group. This Python application is based on the TargetScan 6.2 microRNA target prediction data. Conserved and Nonconserved site context+ scores files are required (unzip and place to directory with program). Available at http://targetscan.org/cgi-bin/targetscan/data_download.cgi?db=vert_61
