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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://cran.r-project.org/package=pROC
Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Proper citation: proc (RRID:SCR_024286) Copy
https://cran.r-project.org/package=psyphy
Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations.
Proper citation: psyphy (RRID:SCR_024289) Copy
Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO.
Proper citation: ruby-bio (RRID:SCR_024322) Copy
https://cran.r-project.org/web/packages/OptimalCutpoints/index.html
Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.
Proper citation: optimalcutpoints (RRID:SCR_024283) Copy
https://cran.r-project.org/web/packages/rpact/index.html
Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints.
Proper citation: rpact (RRID:SCR_024300) Copy
https://cran.r-project.org/web/packages/shazam/index.html
Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.
Proper citation: shazam (RRID:SCR_024301) Copy
https://github.com/rrwick/Unicycler
Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline.
Proper citation: Unicycler (RRID:SCR_024380) Copy
http://tab2mage.sourceforge.net/
Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database.
Proper citation: tab2mage (RRID:SCR_024359) Copy
Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.
Proper citation: PyBEL (RRID:SCR_017660) Copy
The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.
Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy
http://cudasw.sourceforge.net/
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
Proper citation: CUDASW++ (RRID:SCR_008862) Copy
http://bioen-compbio.bioen.illinois.edu/FusionHunter/
Software for identifying fusion transcripts using paired-end RNA-seq.
Proper citation: FusionHunter (RRID:SCR_011895) Copy
https://github.com/Pithikos/C-Thread-Pool
Software for minimal but powerful thread pool in ANSI C.
Proper citation: C Thread Pool (RRID:SCR_023999) Copy
https://github.com/smirarab/sepp/
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Proper citation: sepp (RRID:SCR_024327) Copy
https://www.teuniz.net/edflib/
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Proper citation: EDFlib (RRID:SCR_024010) Copy
http://www.dclunie.com/dicom3tools.html
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Proper citation: Dicom3tools (RRID:SCR_024008) Copy
https://gitlab.com/kyrgyzov/lsa_slurm
Software tool to implement pre-assembly binning scheme leveraging sparse dictionary learning and matrix factorization to solve sparse decomposition problems arising in field of metagenomics.
Proper citation: lsa_slurm (RRID:SCR_018134) Copy
https://github.com/stamatak/AxPcoords.dist
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Proper citation: AxPcoords (RRID:SCR_023971) Copy
http://sco.h-its.org/exelixis/web/software/AxParafit/index.html
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Proper citation: AxParafit (RRID:SCR_023968) Copy
https://github.com/nextstrain/auspice
Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.
Proper citation: Auspice (RRID:SCR_023966) Copy
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