Search Results for "open any file" - Page 4
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Showing 403 open source projects for "open any file"
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Red Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
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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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HSRA
Hadoop spliced read aligner for RNA-seq data
... is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs. -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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ParBiBit
Parallel tool to search biclusters on binary datasets
ParBiBit is a parallel tool to accelerate the search of biclusters on binary datasets, especially useful for gene expression data. This tool receives as input the expression values of n genes and m samples in a file with ARFF extension and returns a file with the biclustering information. -
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MGF 2 FOR-JSON
Conversion of MGF files to JSON format
Want to convert an MGF file to JSON format? This is the app for you, especially if you want to use the JSON file in the FOR-IDENT search program. If you don't know what MGF file, JSON format, FOR-IDENT search program is then this isn't the app for you. Happy conversion! -
Newsrooms, campaigns and contact management in one powerful tool With Prezly, you can save time on juggling multiple outdated tools like Word docs, plain text email with heavy attachments, and Excel spreadsheets that keep getting longer.
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OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
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Peptide3D 2 MGF
Converter for Peptide3D.xml to MGF
Ever wanted to make an MGF file from a Peptide3D.xml output? If so then this is for you. Simply drag the xml onto the window and that's it. All the information needed is contained within the xml file. You get your mgf in the same place, same name, different extension. -
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D-Tailor
D-Tailor: automated analysis and design of DNA sequences
Recent advances in DNA cloning and synthesis technologies afford high throughput implementation of designed sequences into living cells. However, our ability to design sequences to interrogate multifactorial biological processes and further engineer biological functions is lagging behind. DNA-Tailor (D-Tailor) is a fully extendable software framework for biological sequence analysis and multi-objective sequence design. D-Tailor permits the seamless integration of an arbitrary number of... -
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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 (http...
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QMinim
A web-based minimisation service
Based on MinimPy (http://sourceforge.net/projects/minimpy/), QMinim is a web-based minimization application, for allocation of subject to different arms of a clinical trial. It is an alternative to randomization, with the advantage of balancing arms of trial with respect to preselected prognostic factors. All aspects of minimization procedure including treatments, factors, minimization protocole, and including a preload can be customized using QMinim. -
Save administrative costs with simple time tracking and approvals. Understand with precision how your employees are actually spending their time relative to plan. Gain insights on the performance of your company so you can be more strategic on growing your business. Integrate with your existing CRM, or leverage Nostra's to gain insight on your profits and how your sales pipeline is putting demands on your resources. Make only the hires you have to. Gain early insight your sales pipeline and being intune with all inflight projects, Nostra will guide you on exactly when, what and who to hire for. Track milestones and time entry so you know what you can invoice for and when and get paid on time. With approval workflows and integrations with GL systems, you will not leak any revenue.
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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CNVMM
CNVMM performs copy number variations detection
CNVMM specializes in identifying copy number variations (CNVs) when there are repeated sequences in the reference genome. The input file is a single short read mapping result from any short read aligners. However, NNmapper or Bowtie2, which detect all mapping results for multi-reads, are recommended. To use the code, MATLAB installation is required. Mac or Linus system is required. -
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NNmapper
Perform short reads mapping
NNmapper constructs reference reads library and calculates the Euclidean distances between library reads and query reads. NNmapper can map a query read (1) to the library read that gives the smallest distance (most similar), (2) to the library read that gives the smallest distance while the distance is smaller than a threshold, or (3) all library reads that have distances smaller than threshold. NNmapper has high error-tolerant and is suitable for any read lengths. NN reports all mapping... -
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mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
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EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence. Please download EigenMS.zip file (latest version). Latest version uploaded in October 2017 has a bugfix for single treatment group normalization. Rescaling has been omitted from 2015. EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can...
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gogadget
A toolbox for interpretation and visualization of RNA-seq GO analysis
gogadget is an R package, and can help with the visualization and interpretation of GO enrichment analysis of RNA-seq data. It is developed especially for the use in combination with goseq. The functions that are available in this package are extensively described in the user's guide. To install the package download the "gogadget_2.1.tar.gz" file, open R and install with the following line: install.packages( "C:/your/directory/gogadget_2.1.tar.gz", repos = NULL, type="source... -
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RDML stands for Real-time PCR Data Markup Language and is the standard file format for export, storage and exchange of quantitative PCR (qPCR) data. This project focuses on the development, implementation and enhancement of the RDML file format and its description (XML schema).
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BioRec:Bird Census field data annotation
Recognizing biological data from a notebook.
This project helps to digitize field data for a certain Bird Census method. Namely, bird census based on personal inspection or small (~10 km^2) regions with recording birds' position and behaviour on paper. This project makes it easy to annotate such field data and to make this data available for statistical analysis. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target... -
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Maui
Maui is the Maltcms User Interface
Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas. -
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BOWS
Bioinformatics Open Web Services
BOWS is a generic system based on Web Services which allows programmatic access to applications running on HPC clusters. BOWS allows incorporation of several independent applications since programmers can install them in HPC clusters in any programming language. The lonely requirement is to write a script named “arrow” which calls BOWS back-end services periodically in order to check for new processes and their required parameters. If a new process is found, the “arrow” script should change... -
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WrapImaJ
Multi-platform API for Image Processing systems in Life Sciences
WrapImaJ purposes to be a multi-platform wrapper for different Image Processing systems for: - using the Java programming language. The purpose of WrapImaJ is not to combine an exhaustive collection of all functionalities of different imaging system, but to offer a simple, concise Application Programming Interface (API) - allowing to develop imaging software, the source code of which is independent from the underlying imaging system on which it relies. In it's current form, it... -
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please... -
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The Ontology for Biomedical Investigations (OBI) provides an ontologically well-engineered, integrated set of generic and domain-specific terms for use by different communities, from across the biosciences, using any of a variety of technologies.
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... available as well. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. In case you use the package in your work, we do appreciate a citation to a DSS publication. Citation: Yadav et al. (2014), Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Scientific Reports 4, 5193; DOI:10.1038/srep05193 Please visit the link below for details
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Kinannote
Protein Kinase Identification and Classification
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2...