Search Results for "linux command"
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350 projects for "linux command" with 2 filters applied:
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Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in... -
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SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
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CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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MView
Extract and reformat a sequence database search or multiple alignment
NOTE: The MView repository and web pages have moved to: https://github.com/desmid/mview https://desmid.github.io/mview/ Release tarballs will continue to be uploaded to SourceForge. ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common... -
AI-generated apps that pass security reviewRetool lets you generate dashboards, admin panels, and workflows directly on your data. Type something like “Build me a revenue dashboard on my Stripe data” and get a working app with security, permissions, and compliance built in from day one. Whether on our cloud or self-hosted, create the internal software your team needs without compromising enterprise standards or control.
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
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AMBIT:Chemical Structure DB&Web Service
Chemical structures database & machine learning with web services API
AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials. Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases. -
Forever Free Full-Stack Observability | Grafana CloudBuilt on open standards like Prometheus and OpenTelemetry, Grafana Cloud includes Kubernetes Monitoring, Application Observability, Incident Response, plus the AI-powered Grafana Assistant. Get started with our generous free tier today.
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FullSSR
SSR detection and primer designing software
Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step. -
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ntx
Neutrality tests using the SNP site frequency spectrum
Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations. -
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and... -
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ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.
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GenForm
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can... -
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
MANTI is a one-stop shop N-termini annotation & evaluation solution. MANTI was previously (un)known as muda.pl ahead of v3.7, the project was renamed to MANTI.pl with v3.7 on 2019-06-24. It congregates information from different MaxQuant or DiaNN/MSFragger output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred... -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab-delimited text, Percolator pin, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net -
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sdsorter
Easy manipulation of sdf molecular data files.
sdsorter provides convenient routines for manipulating the contents of sdf molecular data files based on the embedded sd tags. -
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite
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MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
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ModST
A tool to search post-translational modifications in a blind mode
ModST (pronounced as modest) is a tool to search post-translational modifications (PTMs) in mass spectrometry data in an unrestrictive manner. It can search for hundreds of modification without any user provided information for variable modifications. Due to data level parallelization implemented through perl it is fast, portable and easy to use to identify and analyse PTMs in MS/MS data. -
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This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.
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IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Please cite: Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. LNBI. 4463:394-405.
