Search Results for "base-files" - Page 6
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Showing 304 open source projects for "base-files"
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Deploy Red Hat Ansible Automation Platform on Microsoft Azure for a strategic automation solution that allows you to orchestrate, govern and operationalize your Azure environment.
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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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... is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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TE-locate
a tool for calling transposons
TE-locate is a tool to locate all copies of sequences in a reference sequence using read-pairs. TE = Transposable Element Input is NGS-data. Please download all files first (including the demo data) and make your first run then. -
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A basic and easy java program to make black and white identikit drawing ,with a library of face elements that you can also modify and expand without limit !Source code available. Also available a very rough base for a 3D construction of the face.
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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... -
As your users rely more and more on Cloud and Internet-based technologies, reliable internet connectivity becomes more and more important to your business. With Bigleaf’s proven SD-WAN architecture, groundbreaking AI, and DDoS attack mitigation, you can finally deliver the reliable internet connectivity your business needs without the limitations of traditional networking platforms. Bigleaf’s Cloud Access Network and plug-and-play router allow for limitless control to and from anywhere your traffic needs to go. Bigleaf’s self-driving AI automatically identifies and adapts to any changing circuit conditions and traffic needs—addressing issues before they impact your users. Bigleaf puts you in the driver’s seat of every complaint and support call with full-path traffic and network performance data, delivered as actionable insights, reports, and alerts.
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
... from RNAseq data: preprocess: Generates aligned and recalibrated BAM files. expression: Generates gene expression (RPKM) and quality metrics. fusion: Identifies candidate gene fusions. guess-ft: Supervised search for fusion transcripts. guess-if: Supervised search for intragenic fusions. homology: Calculates homology between given two genes. frame: Predicts functional consequence of fusion transcript -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices... -
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GTFplus
Prediction of SNP > SAP; generation of proteotypic peptides
This tools translates mRNA transcripts containing mutations of SNP in the VCF format. It accepts Annovar annotation files and incrorporates them into a single table containing translated SNPs. GTFplus predicts potential proteotypic peptides basing on the uniquness of the sequence. -
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This script can convert raw diffraction images to JPEG files. Support ADSC, MarCCD, Mar345, RAXIS and PILATUS, and can be run on Windows, Linux and Mac OS X.
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VANTED - Visualization and Analysis of NeTworks containing Experimental Data At SourceForge the VANTED development history is preserved, only limited amount of development will proceed here. Please head on to the most recent developments, which can be observed at www.vanted.org.
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Engage is a pre-built, intelligent contact center platform that transforms customer service.
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Visual Blast
GUI to accelerate protein and nucleotide BLAST analysis
BLAST (Basic Local Alignment Search Tool) is a popular program that retrieves a library of sequences that resemble the query. The major problem experienced by new users of BLAST revolves around constructing syntactically and semantically correct command line, getting input files into acceptable formats and assessing the output. Visual BLAST is a Graphical User Interface written in C# and it was developed to simplify the parameters setting for BLAST searches. Visual BLAST aims to make BLAST... -
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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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Marta
Cancer Registry Web Application
Marta è una web application nata per aiutare i Registri Tumori. Accesso sicuro alle informazioni, tool di importazione, algoritmi di analisi e molto altro. Ma ho bisogno di una mano...da solo non ho abbastanza tempo ! Se volete aiutare, contattatemi su: - **gmail/hangout** dangeloantonio179@gmail.com - **skype** sickpuppies73 Più ne siamo e meglio è ! -
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss... -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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chromgenie
A tool to correlate gene expression changes with epigenetic changes
Changes in cellular gene expression may occur in response to stimuli or development. There may be simultaneous changes in histone marks and transcription factor binding. How these relate to gene expression changes is often unclear. This tool was written to detect correlations between changes in gene expression between two conditions and concurrent changes in histone marks or transcription factor binding events. The user supplies three files. 1. A tab delimited file of gene expression... -
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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 -
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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... -
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BlastFilter
Extract good and bad alignments into different files using BLAST+.
BlastFilter uses NCBI BLAST+ to compare sequences to a references. With the threshold set by the user using percentage of identity, the software extract the subject sequences into separate fasta files (good vs bad alignments). -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
... the homozygous regions and then search for the disease gene by sequencing the genes within this candidate disease loci. Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf files as an input file, our program identifies the majo -
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dna-bison
Bisulfite alignment On Nodes of a cluster
... on github (https://github.com/dpryan79/bison). There is now a tutorial available in the downloads here: http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download . -
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iMS2Flux is a command line based high-throughput processing tool set for stable isotope labelled mass spectral data targeting metabolic flux analysis. To get started simply download and unzip the iMS2Flux.zip file and follow the getting started document for your OS. Current version 7.2.1 (last updated 9/30/2014) - Completes support and correction functionality for a new user specified generic data class. See the change log for full details.
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GUDM
A tool for pre-processing and fusing heterogeneous datasets
Global Unified Data Modeler (GUDM) is a bioinformatics software tool used for pre-processing and integrating multiple heterogeneous datasets, collected from multi-modal sources, into an integrated dataset. This integrated dataset is supposed to be used for different types of medical analysis and unified decisions, using different machine learning approaches. -
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mullpy
Multilabel-learning library built on python
Mullpy is a machine-learning library that mainly aim to solve multi-label problems. It is classifier independent, has many ensemble capabilities (diversity methods like bagging, random subspaces, etc.) and automated results presentation (Excel, images as ROC or class-separated info, etc.). It is fully configurable. At the moment supports Neural Networks and classifiers defined in files. It is working on python3.3. -
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Athus
Manage, merge, filter and convert population genetics data
... call files) * work with genetic maps ... -
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deFuse is a software package for gene fusion discovery using RNA-Seq data. deFuse .tar.gz bundles will be released periodically on the sourceforge site, see Files. Questions can be posted to the sourceforge discussion forum. The sourceforge wiki is depracated in favour of documentation included with the package. Development of deFuse is on the bitbucket site, linked below.