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https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/
Software tool to correct sequencing errors in single pass reads for de novo assembly.
Proper citation: sprai (RRID:SCR_024353) Copy
https://intel.github.io/scikit-learn-intelex/latest/
Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications.
Proper citation: scikit-learn-intelex (RRID:SCR_024595) Copy
https://github.com/streamlit/streamlit
Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.
Proper citation: streamlit (RRID:SCR_024354) Copy
https://cme.h-its.org/exelixis/web/software/sweed/
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Proper citation: sweed (RRID:SCR_024357) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-TCoffee
Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.
Proper citation: Bio-Tools-Run-Alignment-TCoffee (RRID:SCR_024070) Copy
https://github.com/magnusmanske/snpomatic
Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,
Proper citation: snpomatic (RRID:SCR_024348) Copy
https://www.certara.com/software/phoenix-pkpd/
Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.
Proper citation: WinNonlin (RRID:SCR_024504) Copy
https://github.com/harvardinformatics/NGmerge
Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates.
Proper citation: NGmerge (RRID:SCR_024483) Copy
Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.
Proper citation: Workrave (RRID:SCR_024364) Copy
http://xmedcon.sourceforge.net/
Open source software toolkit for medical image conversion.
Proper citation: XMedCon (RRID:SCR_024366) Copy
http://www.ks.uiuc.edu/Research/vmd/
Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
Proper citation: VMD (RRID:SCR_024368) Copy
Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions.
Proper citation: DNA Amplicon (RRID:SCR_024481) Copy
https://github.com/miRTop/mirtop
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Proper citation: mirtop (RRID:SCR_024116) Copy
https://sourceforge.net/projects/mpsqed/
Software tool for the design of multiplex pyrosequencing assays.
Proper citation: mPSQed (RRID:SCR_024118) Copy
http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.
Proper citation: SMILE (RRID:SCR_024119) Copy
Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.
Proper citation: PKD Foundation (RRID:SCR_000209) Copy
http://research.mssm.edu/cnic/tools-rayburst.html
A software application which provides the source code for the Rayburst Algorithm. The fully automated algorithm casts rays in a 2D/3D dataset without the use of pre-generated ray tables. It is implemented in ANSI C as a single module. The most current version is Version 1.1, last updated on Aug. 15, 2006.
Proper citation: Rayburst Open-Source Code (RRID:SCR_013799) Copy
http://faculty.washington.edu/browning/presto/presto.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)
Proper citation: ENDOG (RRID:SCR_013289) Copy
http://wpicr.wpic.pitt.edu/WPICCompGen/fdr/
Software application (entry from Genetic Analysis Software)
Proper citation: WEIGHTED FDR (RRID:SCR_013442) Copy
http://www.openbioinformatics.org/gengen/
A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated.
Proper citation: GenGen (RRID:SCR_013447) Copy
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