Tools   Select Another Resource Report Type

https://www.bioworlde.com/

An Antibody supplier

Proper citation: Bioworld Technology (RRID:SCR_005036) Copy   

•   Source: SciCrunch Registry

http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/

A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.

Proper citation: SSPACE (RRID:SCR_005056) Copy   

•   Source: SciCrunch Registry

http://meringlab.org/software/hpc-clust/

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

Proper citation: HPC-CLUST (RRID:SCR_005052) Copy   

•   Source: SciCrunch Registry

http://www.manchester.ac.uk/

Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment.

Proper citation: University of Manchester; Manchester; United Kingdom (RRID:SCR_004996) Copy   

•   Source: SciCrunch Registry

https://bxcell.com/

Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.

Proper citation: Bio X Cell (RRID:SCR_004997) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/sunyijun/ES-Tree.htm

Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time.

Proper citation: ESPRIT-Tree (RRID:SCR_005045) Copy   

•   Source: SciCrunch Registry

http://www.cuni.cz/UKEN-1.html

Research university located in Prague, Czech Republic.

Proper citation: Charles University; Prague; Czech Republic (RRID:SCR_002931) Copy   

•   Source: SciCrunch Registry

http://biohealth.snu.ac.kr/software/TRAP/

A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

Proper citation: Time-series RNA-seq Analysis Package (RRID:SCR_002935) Copy   

•   Source: SciCrunch Registry

http://www.genscript.com

Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.

Proper citation: GenScript (RRID:SCR_002891) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pBuild/index.html

A software tool that can compare several search engines' results and combine them together.

Proper citation: pBuild (RRID:SCR_002929) Copy   

•   Source: SciCrunch Registry

http://www.nationalpostdoc.org/

Representative organization for postdoctoral scholars in the United States. It is member-driven and non-profit.

Proper citation: National Postdoctoral Association (RRID:SCR_002928) Copy   

•   Source: SciCrunch Registry

https://github.com/GiBacci/StreamingTrim/

A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.

Proper citation: StreamingTrim (RRID:SCR_002922) Copy   

•   Source: SciCrunch Registry

http://www.mrn.org/

Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility.

Proper citation: Mind Research Network (RRID:SCR_002925) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pLabel/index.html

Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pLabel (RRID:SCR_002923) Copy   

•   Source: SciCrunch Registry

https://github.com/itojal/hot_scan

A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.

Proper citation: hot scan (RRID:SCR_002840) Copy   

•   Source: SciCrunch Registry

http://www.celgene.com

An American global biotechnology company that manufactures drug therapies for cancer and inflammatory disorders. The company's major products are Thalomid (thalidomide), which is approved for the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL), as well as in combination with dexamethasone for patients with newly diagnosed multiple myeloma, and Revlimid (lenalidomide), for which the company has received FDA and EMA approval in combination with dexamethasone for the treatment of multiple myeloma patients who have received at least one prior therapy. Revlimid is also approved in the United States for the treatment of patients with transfusion-dependent anemia due to Low- or Intermediate-1-risk Myelodysplastic syndromes (MDS) associated with a deletion 5q cytogenetic abnormality with or without additional cytogenetic abnormalities. Both Thalomid and Revlimid are sold through proprietary risk-management distribution programs to ensure safe and appropriate use of these pharmaceuticals. Vidaza is approved for the treatment of patients with MDS. Celgene also receives royalties from Novartis Pharma AG on sales of the entire Ritalin family of drugs, which are widely used to treat Attention Deficit Hyperactivity Disorder (ADHD). (Adapted from Wikipedia) There are numerous clinical trials at major medical centers using compounds from Celgene. Investigational compounds are being studied for patients with incurable hematological and solid tumor cancers, including multiple myeloma, myelodysplastic syndromes, chronic lymphocyte leukemia (CLL), non-Hodgkin's lymphoma (NHL), glioblastoma, and ovarian, pancreatic and prostate cancer.

Proper citation: Celgene (RRID:SCR_002955) Copy   

•   Source: SciCrunch Registry

http://rdock.sourceforge.net/

A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.

Proper citation: rDock (RRID:SCR_002838) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Proper citation: Basic4Cseq (RRID:SCR_002836) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/SMRT-Analysis/

Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.

Proper citation: SMRT-Analysis (RRID:SCR_002942) Copy   

•   Source: SciCrunch Registry

http://www.the-aps.org/

A nonprofit devoted to fostering education, scientific research, and dissemination of information in the physiological sciences. Founded in 1887 with 28 members, the APS now has over 10,500 members. Most members have doctoral degrees in physiology and/or medicine (or other health professions). APS is governed by an elected Council consisting of a President, President-Elect, Past President, and nine Councillors. The National headquarters of the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for Experimental Biology (FASEB). The American Physiological Society Awards program demonstrates the Society's dedication to its members and biomedical research by recognizing the research efforts of outstanding APS members. Awards are offered by the Society and the various APS Sections. For questions regarding the Society awards (including Student awards), please send an email to awards_at_the-aps.org. For questions regarding the Section awards please contact the individual Sections directly www.the-aps.org/sections/.

Proper citation: American Physiological Society (RRID:SCR_002826) Copy   

•   Source: SciCrunch Registry