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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.
http://www1.montpellier.inra.fr/CBGP/diyabc/
Software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data.
Proper citation: DIYABC (RRID:SCR_012031) Copy
https://sites.google.com/site/famannotation/home
An automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies.
Proper citation: FamAnn (RRID:SCR_012032) Copy
http://pathways.mcdb.ucla.edu/algal/
Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.
Proper citation: Algal Functional Annotation Tool (RRID:SCR_012034) Copy
https://code.google.com/p/metextract/
A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry.
Proper citation: MetExtract (RRID:SCR_012048) Copy
http://mzmine.sourceforge.net/
Software for mass-spectrometry data processing, with the main focus on LC-MS data.
Proper citation: MZmine (RRID:SCR_012040) Copy
https://code.google.com/p/gene-armada/
Software for the analysis of microarray data with a MATLAB implemented platform with a GUI that integrates all steps of microarray data analysis including automated data import, noise correction, filtering, normalization, statistical testing, clustering, classification and annotation.
Proper citation: Gene ARMADA (RRID:SCR_012006) Copy
Community building portal that serves over 3,000 members from more than 70 countries by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment, etc.
Proper citation: International Society for Computational Biology (RRID:SCR_012009) Copy
http://sourceforge.net/projects/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
Online community for industry news and careers for life science professionals.
Proper citation: BioSpace (RRID:SCR_012010) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://tfclass.bioinf.med.uni-goettingen.de/tfclass
Database that classifies human transcription factors based on the characteristics of their DNA-binding domains. It comprises six levels (superclasses, classes, families, subfamilies, genera and factor species), two of which are optional (subfamilies and factor species). The full classification can also be obtained as html document and as ontology in obo-format., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TFClass (RRID:SCR_012018) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
http://www.stat.purdue.edu/~doerge/software/TSPM.R
Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.
Proper citation: TSPM.R (RRID:SCR_012021) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
http://www.nature.com/nmeth/journal/v5/n3/extref/nmeth.1184-S2.pdf
Software for decoding error-correcting barcodes.
Proper citation: Standalone hamming (RRID:SCR_012025) Copy
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