Search Results for "shotgun"
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Showing 33 open source projects for "shotgun"
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MetalManGames
3rd Party Video Games Developer: MetalManGames, titles of games
...The oldest cross-platform games have been removed along with Android, due to updates needed, and currently can not find the time at this moment. So far have included ; ''Undead Shotgun Reloaded'' Linux 64-bit version, needs SDL2 Installed, and download packs; 1- 3, and extract them to the ''lib'' folder, see; readme.txt for more details. "Alien Parasites" will be placed here soon for Linux 64-bit version, I hope. -
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BADASS is a software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes described so far. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. ...
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QuantWiz-IQ is a tool for reporter based MS/MS quantitation using iTRAQ or TMT tags from shotgun proteomics experiments. It supports MGF and HUPO-PSI mzML format as input. It supports quantitation of reporter tags with iTRAQ 4-plex or 8-plex. It also supports TMT 2/6/10-plex quantitation.
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TARGT pipeline
Targeted Analysis of sequence Reads for GenoTyping of HLA/MHC genes
The 'TARGT' pipeline for Targeted Analysis of sequencing Reads for GenoTyping can be used for genotyping of MHC/HLA genes (or other genomic regions) from ancient and modern shotgun sequence data with moderate to low sequence coverage. The pipeline consists of a main bash script that calls the different steps of the pipeline and can either be called directly or submitted to a cluster queue system, as well as additional sub-scripts and files, that are required to perform the different steps. The pipeline also requires installed versions of the mapping tool Bowtie2 and samtools. -
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Bat Attack
Bat Attack is a cool classical 8bit game to save wife from the Bats
...You have to get Betty back by using the guns available to your disposable. When the bats are killed they make a mess all over the ground and sometimes drop weapons they have devoured. There are three weapons available handgun / shotgun / and machine, all useful in there own way. There are three bosses to kill that can be tricky, but don’t let them take your head. -
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...The V4 version released here on SourceForge stay up as some automated release fetching packages rely on V4. MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
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Central Proteomics Facilities Pipeline
A data analysis pipeline for shotgun mass-spectrometry proteomics.
CPFP provides a pipeline for the analysis of MS/MS proteomic data, targeted at the needs of central proteomics facilities. == Project Status - Updated January 3rd 2019 == CPFP has not been actively developed since 2014, when I left the proteomics group at UTSW. To access up-to-date algorithms for the analysis of proteomics data, other tools would now be preferred. However: * Limited fixes have been made on the main master branch by Phil Charles at the University of Oxford. * As... -
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GlycoPAT
Comprehensive, open-source tool for glycoproteomics MS data analysis
GlycoPAT is a modular, open-source MATLAB based toolbox for shotgun mass spectrometry based glycoproteomics data analysis. This program provides a novel platform for the streamlined analysis of traditional LC-MSn based high-throughput experimental data for the identification of site-specific N- and O-linked glycosylation on various proteins. More details are available at https://www.VirtualGlycome.org/glycopat Source code also available at https://github.com/kaichengub/GlycoPAT If you use this software please cite: Gang Liu, Kai Cheng, Chi Y. ... -
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Opera
An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads. An updated version called OPERA-LG has been re-engineered with features for the assembly of large and complex genomes. Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y. ... -
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SUPER-FOCUS
A tool for agile functional analysis of shotgun metagenomic data.
SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances. The tool was tested with over 70 real metagenomes, and the results show that our approach accurately predicts the subsystems present in microbial communities, and it can be up to over 1,000 times faster than other tools. -
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MUMAL2
Multivariate analysis of MS/MS data using ML techniques
Program described in the paper: MUMAL2: Improving sensitivity in shotgun proteomics using cost sensitive artificial neural networks and a threshold selector algorithm, 2016. By Fabio R. Cerqueira; Adilson M. Ricardo; Alcione P. Oliveira; Armin Graber; Christian Baumgartner. -
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Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
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Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
...We demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. -
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biogas_metagenome_binning
perl scripts to extract microbial genomes from metagenome assembly
Metagenomic assembly of shotgun reads generates huge number of scaffolds derived from different microbial genomes present in the community. Binning is the process of grouping scaffolds (or sequence reads) and assign them to the operational taxonomic units. The microbial genomes extracted from the binning procedure are frequently named “genome bins” to discriminate them from microbial genomes obtained from sequencing and assembly of a bacterial clone. -
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AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
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Secret Agent Remake
Remake of old game Secret Agent (more weapons, better AI)
Remake of old game Secret Agent. The idea is much better AI (opponents will run, jump, dodge), different weapons and more. Planned features: - Turrets and traps - Robot enemies - Much improved AI - Dynamic difficulty (based on episode progress, causes more spawned enemies with better AI) - Weapons shop when entering a building - Results screen when finished a building - Inventory items (defuse kit, mines, grenades, medkit) - Cutscenes - Menu (settings, save, load, select... -
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This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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PennCNV-tumor
Inference of copy number variation/abberation
PennCNV-tumor is software that is appropriate for inferring copy number variation or abberations in germline or tumor tissue respectively. It takes in as input data either signal intensity from genotyping microarrays or aligned read counts from shotgun sequencing experiments. The software is written in C++ and targeted for unix/linux platforms. -
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plfdr
Decoy-free protein-level fdr estimation
Statistical validation of protein identifications is an important issue in shotgun proteomics. The false discovery rate (FDR) is a powerful statistical tool in evaluating the protein identification result. Several research efforts have been made for FDR estimation at the protein-level. However, there are still certain drawbacks in the existing FDR estimation methods based on the target-decoy strategy. In this paper we propose a novel method for validating protein identifications without searching a decoy database. -
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PRICE de novo (meta)genome assembler
Targeted de novo assembly of (meta)genomic components
...Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler. PRICE was designed to address the challenge of assembling viral genomes that comprise a small minority of the reads within ultra-deep, short-read, shotgun metagenomic datasets. PRICE has already enabled the discovery of several novel virus genomes from such complex datasets, and it is also being applied to the de novo assembly of large individual genomes. -
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Classic Alphas and Betas
The alpha and beta versions of the PC classics
As of 31-Dec-2012, this repository has had a huge facelift, I've cleaned up the directories and uploaded the installer versions of the alpha, and also added the beta. You can also access the source code via the SVN. As of 1/01/2013, to celebrate the new year, I've changed this repo to not be Blood exclusive. I will also now be hosting the following alphas\betas: - Shadow Warrior beta - Duke Nukem 3D beta - Duke Nukem 3D alpha - Doom alphas (0.2, 0.4, 0.5, press-release) All... -
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