Search Results for "bio-bwa" - Page 5
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Showing 346 open source projects for "bio-bwa"
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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Chat with your business data with Looker. More than just a modern business intelligence platform, you can turn to Looker for self-service or governed BI, build your own custom applications with trusted metrics, or even bring Looker modeling to your existing BI environment.
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dna-bison
Bisulfite alignment On Nodes of a cluster
Bison allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. It can align both directional and non-directional libraries and uses bowtie2. Multiple compute nodes are not absolutely required, but will make the alignment process faster. Further details available on the Wiki page. Help also available on SEQanswers (http://seqanswers.com/forums/showthread.php?t=31314) or by creating a ticket here. You can now track the... -
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smalt
A mapper for DNA sequencing reads
SMALT aligns DNA sequencing reads with genomic reference sequences. It employs hashing combined with dynamic programming. -
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ExonFinder
A pipeline to extract novel cassette exons/retained-introns
ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat. -
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Fast Alignment Search Tool suite. A fast sequence read mapper suite for short reads generated with the Illumina platform. Contains mrFAST and mrsFAST. Joint development by University of Washington and Simon Fraser University
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BrightGauge, a ConnectWise solution, was started in 2011 to fill a missing need in the small-to-medium IT Services industry: a better way to manage data and provide the value of work to clients. BrightGauge Software allows you to display all of your important business metrics in one place through the use of gauges, dashboards, and client reports. Used by more than 1,800 companies worldwide, BrightGauge integrates with popular business solutions on the market, like ConnectWise, Continuum, Webroot, QuickBooks, Datto, IT Glue, Zendesk, Harvest, Smileback, and so many more. Dig deeper into your data by adding, subtracting, multiplying, and dividing one metric against another. BrightGauge automatically computes these formulas for you. Want to show your prospects how quick you are to respond to tickets? Show off your data with embeddable gauges on public sites.
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FLASH
Merge mates from fragments that are shorter than twice the read length
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast tool to merge paired-end reads from fragments that are shorter than twice the length of reads. The extended length of reads has a significant positive impact on improvement of genome assemblies. -
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XNBC: neurobiology simulation tool
XNBC is a graphic application to simulate biologic neural networks.
XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows. Web site : http://ticemed-sa.upmc.fr/xnbc/ All recent versions are on this site. -
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wEMBOSS is a Web interface for the EMBOSS software package for biological sequence analysis. Under wEMBOSS each user has a private workspace (UNIX home directory) on the server, where he can permanently store his data and organize them in projects. The companion suite wrappers4EMBOSS allows to integrate under EMBOSS a number of popular bioinformatic software suites as BLAST, CLUSTAL and MRS.
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leave-kojack
Leave-k-out-Jackknife Pearson correlation
In general, Pearson correlation coefficients can be quite error-prone to outliers, thus Jackknifing may be helpful. I could not find any useful implementation for calculating more than leave-1-out Jackknife Pearson correlation coefficients. 'leave-kojack' offers an implementation for Jackknife Pearson correlation with dynamic values of k, i.e. leave-k-out Pearson correlation. -
Collaborate is customizable case management software for non-profits and social services agencies with teams of 5+ staff.
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A Scalable Multicore Code for RNA Secondary Structure Prediction
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This is a project for Andre to share CellML related tools he works on that other people might find useful.
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MolSig
The Stereo Signature Molecular Descriptor
An algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure, based on our previously introduced signature molecular descriptor. The algorithm can generate two types of descriptors, one which is compliant with the Cahn-Ingold-Prelog priority rules, and a faster one based on our previous definition of a directed acyclic graph that isaugmented to a chiral molecular graph. -
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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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Gene Ontology Browser
Browser for viewing Gene Ontology (GO) .obo files.
Go Browser allows you to view a gene ontology on your local machine. You can go up and down the hierarchy and inspect the terms. It's a good way of familiarising yourself and orienting yourself in the GO system. It's built using the Baby X toolkit, so has no dependencies other than xlib. Baby X has now also been ported to Windows, so a Windows version is available. -
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pmutualinformation
Computes pairwise genes mutual information using GEPs
pmutualinformation (parallel mutual information) computes the pairwise Mutual Information for all pairs of genes from a potentially massive and heterogeneous dataset containing GEPs. GEPs can be part of different experiments collected from public repositories. pmutualinformation runs on MIMD systems and has been implemented in C using the MPI standard. -
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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alnfix
Program to fix issues with helicos bam files.
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x2fasta
Tools for reformatting common sequence formats into fasta
A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format. -
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GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.
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[DEPRECATED] Gene Ontology
The DEPRECATED legacy location of the GO, see http://geneontology.org
The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads. -
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fqzcomp
A fastq compression program
Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels. -
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msBayes allows complex and flexible phylogeographic inference. More specifically, you can test the simultaneous divergence (TSD) of multiple population (species) pairs. It uses approximate Bayesian computation (ABC) under a hierarchical model.
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CSEA
Correcting Structural Errors After Genome Assembly
CSEA is a suite of programs for correcting structural errors after assembly without reference, improve the quality of genome assembly. The program is specially designed for second-generation sequencing reads. It also can do denovo assembly and correct errors. Contact: jbtangcn@gmail.com -
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The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net
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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.