Showing 11 open source projects for "a i"

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  • 1
    BioXTAS RAW

    BioXTAS RAW

    Processing and analysis of Small Angle X-ray Scattering (SAXS) data.

    BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis...
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    Downloads: 97 This Week
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  • 2

    miRge3

    Comprehensive analysis of small RNA sequencing data

    An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). ...
    Downloads: 10 This Week
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  • 3

    reditools

    RNA editing detection by NGS data

    ...RNA editing is a post-transcriptional phenomenon involving the insertion/deletion or substitution of specific bases in precise RNA localizations. In human, RNA editing occurs by deamination of cytosine to uridine (C-to-U) or mostly by the adenosine to inosine (A-to-I) conversion through ADAR enzymes. A-to-I substitutions may have profound functional consequences and have been linked to a variety of human diseases including neurological and neurodegenerative disorders or cancer. NGS technologies offer a unique opportunity to investigate RNA editing. REDItools are simple python scripts conceived to investigate RNA editing at large-scale. ...
    Downloads: 2 This Week
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  • 4

    mitoMaker

    mitoMaker - a mitochondria pipeline wrapper script

    ...It could be used with other targets, such as specific genes, or transcriptomes, even though that is not it's primary goal, nor thoroughly tested. After various attempts to build different mitochondrial genomes in the lab I studied, a general pipeline started to appear: assemble reads with MIRA or SOAPdenovo-Trans, look for a scaffold/contig that matches a closely-related species, check it to see if all expected genomic features are present (since mitochondria is well conserved), check to see if the assembly might have circularized (since it's a circular DNA). ...
    Downloads: 0 This Week
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  • Iris Powered By Generali - Iris puts your customer in control of their identity. Icon
    Iris Powered By Generali - Iris puts your customer in control of their identity.

    Increase customer and employee retention by offering Onwatch identity protection today.

    Iris Identity Protection API sends identity monitoring and alerts data into your existing digital environment – an ideal solution for businesses that are looking to offer their customers identity protection services without having to build a new product or app from scratch.
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  • 5
    EASER

    EASER

    Ensembl Easy Sequence Retriever

    Maldonado E, Khan I, Philip S, Vasconcelos V, Antunes A (2013) EASER: Ensembl Easy Sequence Retriever. Evolutionary Bioinformatics, 9:487-490. doi: https://doi.org/10.4137/EBO.S11335.
    Downloads: 0 This Week
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  • 6

    AMBIENT

    Find active modules in metabolic networks using high-throughput data

    IMPORTANT: Since publication of the AMBIENT method in BMC Sys Bio, several updates have been made. If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. ...
    Downloads: 0 This Week
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  • 7
    Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
    Downloads: 0 This Week
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  • 8

    Pysimony

    A Pythonic Implementation of Parsimony Inference of Phylogeny

    ...As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel
    Downloads: 0 This Week
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  • 9
    Prediction of MHC class I- and MHC class II-restricted T-cell epitopes. Prediction of proteasomal/immunoproteasomal processing of antigens. Prediction of peptide-TAP binding.
    Downloads: 0 This Week
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  • 10
    GUI program to perform multiple searches on proteins for specific groups of amino acids in specific protein regions and to be able to filter by signalp scores. I hope to add lots of new functionality including the ability to create local database
    Downloads: 0 This Week
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  • 11
    Tools and programs I have written for various purposes and those used in it.
    Downloads: 2 This Week
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