Tools   Select Another Resource Report Type

https://uni-freiburg.de/

Public research university located in Freiburg im Breisgau, Baden-Württemberg, Germany.

Proper citation: University of Freiburg; Baden-Wurttemberg; Germany (RRID:SCR_004825) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.sfu.ca/software-variation-hunter

A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.

Proper citation: VariationHunter (RRID:SCR_004865) Copy   

•   Source: SciCrunch Registry

http://www.bostonbiochem.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2021. An Antibody supplier.

Proper citation: Boston Biochem (RRID:SCR_004761) Copy   

•   Source: SciCrunch Registry

http://www.unige.it/

UniGe, is one of the largest universities in Italy. It is located in the city of Genoa and regional Metropolitan City of Genoa, on the Italian Riviera in the Liguria region of northwestern Italy. The original university was founded in 1481.

Proper citation: University of Genoa; Genoa; Italy (RRID:SCR_004878) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/xnat_extras

User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org

Proper citation: XNAT Extras (RRID:SCR_004759) Copy   

•   Source: SciCrunch Registry

http://www.cbcb.umd.edu/software/phymm/

Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.

Proper citation: Phymm and PhymmBL (RRID:SCR_004751) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/destruct/

A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.

Proper citation: deStruct (RRID:SCR_004747) Copy   

•   Source: SciCrunch Registry

http://sri.com/

Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977.

Proper citation: Stanford Research Institute International (RRID:SCR_004926) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/neo/

A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.

Proper citation: Neo (RRID:SCR_000634) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/bsg/software/BEBaC/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.

Proper citation: BEBaC (RRID:SCR_000621) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/flipflop.html

Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

Proper citation: FlipFlop (RRID:SCR_000625) Copy   

•   Source: SciCrunch Registry

http://cryptogenome.ucsf.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco

Proper citation: CryptoBase (RRID:SCR_000780) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/glycoworkbench/

A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.

Proper citation: GlycoWorkbench (RRID:SCR_000782) Copy   

•   Source: SciCrunch Registry

https://www.wool.com/

Company focused on animal welfare and pest prevention in the wool industry.

Proper citation: Australian Wool Innovation Limited (RRID:SCR_000775) Copy   

•   Source: SciCrunch Registry

Discontinued

https://github.com/PacificBiosciences/blasr

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BLASR (RRID:SCR_000764) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmcloser/

Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

Proper citation: GMcloser (RRID:SCR_000646) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/detecttd/

Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.

Proper citation: detecttd (RRID:SCR_000681) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fastuniq/

A software tool for removal of de novo duplicates in paired short DNA sequences.

Proper citation: FastUniq (RRID:SCR_000682) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/4474950

A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.

Proper citation: Sequencing Analysis Software (RRID:SCR_000718) Copy   

•   Source: SciCrunch Registry

http://psychiatry.stanford.edu/

A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine.

Proper citation: Stanford University Psychiatry and Behavioral Sciences (RRID:SCR_000719) Copy   

•   Source: SciCrunch Registry