The Experts below are selected from a list of 1089 Experts worldwide ranked by ideXlab platform

Bruce Ravel - One of the best experts on this subject based on the ideXlab platform.

  • atoms crystallography for the x ray absorption spectroscopist
    Journal of Synchrotron Radiation, 2001
    Co-Authors: Bruce Ravel
    Abstract:

    ATOMS is a user application providing crystallographic functionality useful to x-ray absorption spectroscopists. ATOMS is also a set of reusable, object-oriented software modules written in the Perl Programming Language providing crystallographic functionality and access to databases of absorption coefficients and anomalous scattering factors. The main use of the ATOMS program is to generate input data for the ab initio, multiple scattering, x-ray absorption spectroscopy code FEFF. However the code offers many additional features, including useful calculations involving absorption coefficients and simulations of Diffraction Anomalous Fine-Structure (DAFS) spectra. Command line, graphical, and web-based interfaces to the code are offered as part of the standard distribution. As Perl runs on a wide variety of common computer platforms, ATOMS itself is a cross platform application. All text presented to the user can be internationalized - support for four Languages is currently included in the package. Development of ATOMS is active - a FEFF interface, structure visualization, and additional crystallographic calculations are among the future developments.

  • ATOMS: crystallography for the X‐ray absorption spectroscopist
    Journal of Synchrotron Radiation, 2001
    Co-Authors: Bruce Ravel
    Abstract:

    ATOMS is a user application providing crystallographic functionality useful to x-ray absorption spectroscopists. ATOMS is also a set of reusable, object-oriented software modules written in the Perl Programming Language providing crystallographic functionality and access to databases of absorption coefficients and anomalous scattering factors. The main use of the ATOMS program is to generate input data for the ab initio, multiple scattering, x-ray absorption spectroscopy code FEFF. However the code offers many additional features, including useful calculations involving absorption coefficients and simulations of Diffraction Anomalous Fine-Structure (DAFS) spectra. Command line, graphical, and web-based interfaces to the code are offered as part of the standard distribution. As Perl runs on a wide variety of common computer platforms, ATOMS itself is a cross platform application. All text presented to the user can be internationalized - support for four Languages is currently included in the package. Development of ATOMS is active - a FEFF interface, structure visualization, and additional crystallographic calculations are among the future developments.

Mukesh Jain - One of the best experts on this subject based on the ideXlab platform.

  • NGS QC toolkit: A toolkit for quality control of next generation sequencing data
    PLoS ONE, 2012
    Co-Authors: Ravi K. Patel, Mukesh Jain
    Abstract:

    Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl Programming Language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

Eric J. Nestler - One of the best experts on this subject based on the ideXlab platform.

  • EJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One
    2016
    Co-Authors: Li Shen, Ning-yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J. Nestler
    Abstract:

    ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification ‘‘hotspots’’. diffReps is developed in Perl Programming Language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data

  • diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.
    PloS one, 2013
    Co-Authors: Li Shen, Ning-yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J. Nestler
    Abstract:

    ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs. control, and identify regions that show differences in ChIP enrichment. We have developed a powerful and easy to use program, called diffReps, to detect those differential sites from ChIP-seq data, with or without biological replicates. In addition, we have developed two useful tools for ChIP-seq analysis in the diffReps package: one for the annotation of the differential sites and the other for finding chromatin modification “hotspots”. diffReps is developed in Perl Programming Language and runs on all platforms as a command line script. We tested diffReps on two different datasets. One is the comparison of H3K4me3 between two human cell lines from the ENCODE project. The other is the comparison of H3K9me3 in a discrete region of mouse brain between cocaine- and saline-treated conditions. The results indicated that diffReps is a highly sensitive program in detecting differential sites from ChIP-seq data.

Matthew Newville - One of the best experts on this subject based on the ideXlab platform.

  • ATHENA , ARTEMIS , HEPHAESTUS : data analysis for X-ray absorption spectroscopy using IFEFFIT
    Journal of Synchrotron Radiation, 2005
    Co-Authors: Barbara Ravel, Matthew Newville
    Abstract:

    A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl Programming Language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.

Giovanni Baiocchi - One of the best experts on this subject based on the ideXlab platform.

  • Using Perl for Statistics: Data Processing and Statistical Computing
    Journal of Statistical Software, 2004
    Co-Authors: Giovanni Baiocchi
    Abstract:

    In this paper we show how Perl, an expressive and extensible high-level Programming Language, with network and ob ject-oriented Programming support, can be used in processing data for statistics and statistical computing. The paper is organized in two parts. In Part I, we introduce the Perl Programming Language, with particular emphasis on the features that distinguish it from conventional Languages. Then, using practical examples, we demonstrate how Perl's distinguishing features make it particularly well suited to perform labor intensive and sophisticated tasks ranging from the preparation of data to the writing of statistical reports. In Part II we show how Perl can be extended to perform statistical computations using modules and by "embedding" specialized statistical applications. We provide example on how Perl can be used to do simple statistical analyses, perform complex statistical computations involving matrix algebra and numerical optimization, and make statistical computations more easily reproducible. We also investigate the numerical and statistical reliability of various Perl statistical modules. Important computing issues such as ease of use, speed of calculation, and efficient memory usage, are also considered.