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on page 1 showing 20 out of 1,043 results

Cite this (3D de novo assembly, RRID:SCR_017227)

URL: https://github.com/theaidenlab/3d-dna.git

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

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Cite this (3D Objects Counter, RRID:SCR_017066)

URL: https://imagej.net/3D_Objects_Counter

Resource Type: Resource, software resource, software application, data analysis software, data processing software, image analysis software

Software tool as plugin for ImageJ. Counts the number of 3D objects in stack, quantifies for each found object, generates results representations.

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Cite this (3D Roi Manager, RRID:SCR_017065)

URL: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_roi_manager:start

Resource Type: Resource, software resource, software application, data analysis software, data processing software, image analysis software

Software tool as plugin for ImageJ. Used for 3D objects and image can be segmented directly within plugin via 3D segment button.

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Cite this (ABCDreport, RRID:SCR_016030)

URL: https://github.com/ABCD-STUDY/ABCDreport

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software application as a simple system to review study progress. Used in ABCD study.

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Cite this (AbundantOTU+, RRID:SCR_016527)

URL: http://omics.informatics.indiana.edu/AbundantOTU/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

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    ACQ4

Cite this (ACQ4, RRID:SCR_016444)

URL: http://www.acq4.org/

Resource Type: Resource, software resource, data acquisition software, data analysis software, data processing software, software application

Python-based software for experimental neurophysiology. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques.

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Cite this (AcqKnowledge Software, RRID:SCR_014279)

URL: http://www.biopac.com/product/acqknowledge-software/

Resource Type: Resource, data analysis software, data processing software, software application, software resource, data acquisition software, simulation software

A software program that allows the user to perform data acquistion, stimulation and analyses. Users do not need to know the programming language or a new protocol view. AcqKnowledge Software is compatible with MP150 Research Systems, MP36R Research Systems, and MRI and fMRI Setups. A variety of offline and online analysis tools allows users to customize data recordings and targeted analyses. The software can perform automated analysis routines, output a range of stimulus paradigms, and allows users to record from multiple hardware devices simultaneously.

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Cite this (Activ 2000, RRID:SCR_007352)

URL: http://www.fmritools.org/Activ2000/activ2000.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Data analysis software with the following main features: fMRI spatial and temporal pre-processing (gaussian filtering) with motion correction, time slicing and template co-registration ; fMRI multithreaded bloc processing with one or more conditions (up to 999), lateralization index, paradigm design (box-car style with HRF convolution), anatomic coregistration, multiplanar reconstructions, opengl 3D surfacic rendering. DPTools and Activ 2000 are now one single software: DPTools v 3.0 and above. All the features already included in DPTools are available for the fMRI processings (statistics, motion correction, time slicing, aso). DPTools 3.0 can read Siemens Mosaic and Philips REC/PAR files for diffusion / dynamic series, and can export files to SPM99 format. Features: * Images Conversion * Paradigm Creation * Images Pre-Processing * Images Processing * Statistics * Co-registration * 3D * Filming * Loading / Saving * Batch Script * PACS Integration * and more... Activ 2000 is freely downloadable (46 MB)

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Cite this (AdapterRemoval, RRID:SCR_011834)

URL: https://github.com/MikkelSchubert/adapterremoval

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software program to remove residual adapter sequences from next generation sequencing reads.

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    ADAPT

Cite this (ADAPT, RRID:SCR_006769)

URL: http://bmsr.usc.edu/software/adapt/

Resource Type: Resource, software resource, software application, simulation software, data processing software, data analysis software

Computational modeling platform developed for pharmacokinetic and pharmacodynamic applications. It is intended for basic and clinical research scientists and is designed to facilitate the discovery, exploration and application of the underlying pharmacokinetic and pharmacodynamic properties of drugs. Features in ADAPT 5
*Individual Analysis ** Estimation module (ID) includes weighted least squares, maximum likelihood (ML), generalized least squares (GLS), maximum a posterior Bayesian estimation (MAP) ** Simulation module (SIM) includes capabilities for single and multisubject simulations ** Sample schedule design module (SAMPLE) provides the ability to calculate D- and C-optimal designs * Population Analysis ** Parametric population PK/PD modeling using maximum likelihood estimation via the EM algorithm with sampling (MLEM), as introduced by Schumitzky (1995) and by Walker (1996), with extensions and enhancements by Bauer & Guzy (2004). ** Iterated two-stage (ITS) analysis as proposed by Prevost (1977) and Steimer, Mallet and colleagues (1984). ** Convenient standard two-stage (STS) and naive pooled data (NPD) modeling, each with WLS, ML, and MAP estimators. System Requirements * Operating System: Windows XP/Vista/7 * Other Software REQUIRED: Intel Visual Fortran 10.x XE2013

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Cite this (Adobe Audition, RRID:SCR_015796)

URL: http://www.adobe.com/products/audition.html

Resource Type: Resource, data analysis software, data processing software, software application, software resource, software toolkit, authoring tool

Software for sound analysis, audio editing, and audio recording. It features multitrack, waveform, and spectral display for creating, mixing, editing, and restoring audio content for research or non-research purposes.

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Cite this (Advanced 3D Visualization and Volume Modeling, RRID:SCR_007353)

URL: http://www.fei.com/software/amira-3d-for-life-sciences/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, 3d visualization software, software resource

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

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    Aegean

Cite this (Aegean, RRID:SCR_015965)

URL: http://standage.github.io/AEGeAn

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

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    affydata

Cite this (affydata, RRID:SCR_016976)

URL: http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data or information resource

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

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Cite this (Affymetrix Power Tools, RRID:SCR_008401)

URL: http://www.affymetrix.com/partners_programs/programs/developer/tools/powertools.affx

Resource Type: Resource, software resource, software application, data analysis software, data processing software, commercial organization

Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays. APT is an open-source project licensed under the GNU General Public License (GPL). (Developers who need a non-GPL license may purchase a commercial license from Affymetrix.) APT programs are intended for power users who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. The vision is that APT provides a platform for developing and deploying new algorithms without waiting for the GUI implementations. Sponsors: This resource is supported by Affymetrix, Inc. Keywords: Genomics, Clinical, Study, Bioinformatic, Windows, MacOS, Linux, resource, Data, Normalization, Sequence, Annotation, Gene, Expression, Pattern, Motif, Inference, Toolkit, Model, Fitting, Algorithm,

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    affy

Cite this (affy, RRID:SCR_012835)

URL: http://www.bioconductor.org/packages/release/bioc/html/affy.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

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Cite this (Agilent ChemStation Software, RRID:SCR_015742)

URL: https://www.agilent.com/cs/library/usermanuals/Public/G2070-91126_Understanding.pdf

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data acquisition software

THIS RESOURCE HAS BEEN DISCONTINUED. Documented October 3, 2017.

Operational software created by Agilent Technologies to operate with its ChemStation hardware. The software can manage all parameters for instrument control, data acquisition
and evaluation, including integration, quantification and reporting.

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Cite this (Agilent Masshunter Quantitative Analysis software, RRID:SCR_015040)

URL: http://www.agilent.com/en-us/products/software-informatics/masshunter-suite/masshunter/masshunter-software

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software for the analysis of mass spectrometry data. MassHunter also works with software-specific packages to do more specialized analysis tasks.

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Cite this (Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS, RRID:SCR_016657)

URL: https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Resource Type: Resource, data analysis software, data processing software, software application, data analytics software, software toolkit, software resource, data acquisition software

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

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Cite this (ALGEN-PROMO, RRID:SCR_016926)

URL: http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

Resource Type: Resource, organization portal, data analysis software, data processing software, software application, sequence analysis software, laboratory portal, service resource, portal, software resource, data or information resource

Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches.

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