Search Results for "sam" - Page 2
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Showing 92 open source projects for "sam"
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Jennifer
Crystal ORM using ActiveRecord pattern with flexible query DSL
...Jennifer allows you to maintain everything for your models - from DB migrations and field mapping to callbacks and building queries. For detailed information see the docs and API documentation. For command management Jennifer uses Sam. Due to this you can easily create/migrate/drop a database or invoke a generator to bootstrap your models and migrations. Jennifer has a built-in database migration management system. Migrations allow you to organize all database changes. -
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should then... -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1. Vengadesan, K. & Gautham, N. ...
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SCVZ menza
App za prikaz jelovnika u studentskoj menzi u Varaždinu
Aplikacija napravljena u Flutter framework-u. Projekt koji sam radio u slobodno vrijeme i želim predstaviti prilikom prijave za studentsku praksu. Aplikacija komunicira s Flask serverom koji scrape-a podatke sa službene stranice menze. Server aplikaciji vraća json u kojoj se nalazi današnji jelovnik. Trenutno je server hostan na Heroku platformi. https://scvzmenza-app.herokuapp.com/danas -
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SAM Linux Portable
A portable 64bit Linux system based on Porteus Linux in EN/DE/FR/ES
additional information: Password for guest is "guest" Password for root is "toor" For now you can find more info about the possibilities at the Porteus Website: http://www.porteus.org/info/tips-and-tricks.html . -
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SAMFF
A Refined Empirical Force Field to Model Protein-SAM Interactions
...The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the adsorption orientation of lysozyme on CH3-SAM. For details, please refer to our publication: Bhadra and Siu, "A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF" (submitted) https://cbbio.online/software/SAMFF/index.html -
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go-ipfs-plugin-i2p-gateway
A plugin for presenting an IPFS gateway over i2p
...It simply takes advantage of the plugin system to set up some hidden services when the IPFS plugin is initialized. It does this by reading the IPFS config file to find the ports that have been configured by the admin running IPFS, then using the SAM API to forward those ports to I2P. Once they are forwarded, a config file is generated containing the i2p configuration and it's base32 and base64 addresses. This is stored in a file called "i2pconfig." Finally, it simply forwards the IPFS gateway to I2P. -
Error to trace to log to deploy. One click. No SSH.AppSignal links every error to the trace, the trace to the log, the log to the deploy that shipped it.
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CONDEL is a method for detecting CNVs and deletion types from single samples using high-throughput sequence data. It can be used for analyzing genomes from tumor cells or normal cells with an input of genome reference, reference index, SAM file, and read counts.
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PySptools
Hyperspectral algorithms for Python
...New for v0.14.x: a scikit-learn bridge (alpha and partial). The functions and classes are organized by topics: * abundance maps: FCLS, NNLS, UCLS * classification: AbundanceClassification, NormXCorr, KMeans SAM, SID, SVC * detection: ACE, CEM, GLRT, MatchedFilter, OSP * distance: chebychev, NormXCorr, SAM, SID * endmembers extraction: ATGP, FIPPI, NFINDR, PPI * material count: HfcVd, HySime * noise: Savitzky Golay, MNF, whiten * sigproc: bilateral * sklearn: HyperEstimatorCrossVal, HyperSVC and others * spectro: convex hull quotient, features extraction (tetracorder style), USGS06 lib interface * util: load_ENVI_file, load_ENVI_spec_lib, corr, cov and others The library do an extensive use of the numpy numeric library and can achieve good speed. ... -
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CoVaMa
Co-Variation Mapper
CoVaMa (Co-Variation Mapper) (python) detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
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ScummVM
A cross-platform interpreter for many point-and-click adventure games
ScummVM is a cross-platform interpreter for many point-and-click adventure games. This includes LucasArts SCUMM games (such as Monkey Island 1-3, Day of the Tentacle, Sam & Max, ...), many of Sierra's AGI and SCI games (such as King's Quest 1-6, Space Quest 1-5, ...), Discworld 1 and 2, Simon the Sorcerer 1 and 2, Beneath A Steel Sky, Lure of the Temptress, Broken Sword 1 and 2, Flight of the Amazon Queen, Gobliiins 1-3, The Legend of Kyrandia 1-3, many of Humongous Entertainment's children's SCUMM games (including Freddi Fish and Putt Putt games) and many more. ... -
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endpoint-health
Standalone web application allowing to monitor end points availability
...This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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sfbf
Useful console application to search for largest files on file systems
...It brings features such as : - Fast file search to locate largest files - Configurable search depth - Various output formats (txt, json, xml, html, csv) - Regular expression matching This project is licensed under the WTFPL (Do What The Fuck You Want To Public License, Version 2) Copyright © 2017 spypunk spypunk@gmail.com This work is free. You can redistribute it and/or modify it under the terms of the Do What The Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See the COPYING file for more details. -
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
...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. With SAM standard as input and an intuitive GUI, even non-experts can accomplish a variety of tasks, from visualization of RNA Seq data, up to sophisticated modification analysis with significance-based candidate calling. -
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converts a SAM file to fasta file. SAM file is a file output from bwa alignment software. It outputs aligned fasta file.
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SeqPig
Use Apache Pig to process your large sequencing datasets!
...It provides import and export functions for file formats commonly used for sequencing data, as well as a collection of Pig user-defined-functions (UDF’s) to help process aligned and unaligned sequence data. Currently SeqPig supports BAM/SAM, FastQ and Qseq input and output. For more information see the manual at http://seqpig.sourceforge.net/ -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
This page is here for archival purpose. Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/... -
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A fork of BOSSA
This is a fork of the BOSSA project by ShumaTech.
BOSSA is a flash programming utility for Atmel's SAM family of flash-based ARM microcontrollers, developed by ShumaTech. The motivation behind BOSSA is to create a simple, easy-to-use, open source utility to replace Atmel's SAM-BA software. This project is a fork, created to temporarily host new modifications to BOSSA until they can be incorporated into the main BOSSA codebase. -
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sameflash
Serial flash tool for Atmel M7 core
This tool written in Java uploads HEX files into microcontroller flash and runs it using SAM-BA protocol, as original Atmel tool fails with modern M7 core chips. SAME70 is now supported. Current version does not program GPNVM bit, so after reset program will not start again - just add few lines of code to do that. -
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Sita Access Manager
Sita Access Manager (SAM) is php based Login System.
Sita Access Manager (SAM) is php based and secure login system. -
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money. ...
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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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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet.
