SciCrunch

uManager

Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

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SciCrunch
13 years ago - by Anonymous

TargetCaller

R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).

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SciCrunch
13 years ago - by Anonymous

MIView

OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

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SciCrunch
13 years ago - by Anonymous

Local Binary Pattern Analysis Tools for MR Brain Images

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

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SciCrunch
13 years ago - by Anonymous

Licensing issues in software and data

Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.

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SciCrunch
13 years ago - by Anonymous

flowFlowJo

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

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SciCrunch
12 years ago - by Anonymous

rTANDEM

An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.

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SciCrunch
12 years ago - by Anonymous

metaMA

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

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SciCrunch
12 years ago - by Anonymous

flowPeaks

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

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SciCrunch
12 years ago - by Anonymous

Convert MNI coordinates to or from XYZ

Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other.

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SciCrunch
13 years ago - by Anonymous

Opal Research

Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.

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SciCrunch
13 years ago - by Anonymous

Random findings from the data

Blog about random findings from data written by Leon French.

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SciCrunch
13 years ago - by Anonymous

Academic Seismic Portal at UTIG

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links.

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SciCrunch
13 years ago - by Anonymous

Polar Geospatial Center

Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions.

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SciCrunch
13 years ago - by Anonymous

BD Biosciences: FACSCalibur Flow Cytometry System

Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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SciCrunch
12 years ago - by Anonymous

dbSTS

THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

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SciCrunch
16 years ago - by Anonymous

flowStats

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

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SciCrunch
12 years ago - by Anonymous

Protein-RNA Interaction Database

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2022. It is a repository of interactions found by Entangle and compiled into various tables for use by the RNA community. This data does not have a user interface, but data can be accessed in tables. It contains raw Excel/Access Databases and data processed into useful Figures for people who don't want to wade through the primary data. At present it contains informations from 42 PDBs.

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SciCrunch
17 years ago - by Anonymous

Protein-Protein Interactions Table for Human herpesvirus 1

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The scope of the project includes molecular information pertaining to oral pathogens, bacterial and viral. The website contains a table of protein-protein interactions for human herpesvirus 1. It is operated for the U.S. Department of Energy's National Nuclear Security Administration.

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SciCrunch
17 years ago - by Anonymous

Ulysses

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. System to annotate human genes based on gene interactions in model organisms. Data are transferred from amenable species like yeast, fly, and worm through homology, and functional gene annotation is facilitated through framework of large database. Used to perform interolog analysis by projection of model organism interaction data onto homologous human proteins, and thus serves as an accelerator for analysis of uncharacterized human proteins.

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SciCrunch
17 years ago - by Anonymous

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