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http://www.r-project.org/

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy   

•   Source: SciCrunch Registry

https://github.com/benedictpaten/pecan

A Java consistency based multiple sequence alignment software program.

Proper citation: Pecan (RRID:SCR_001909) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/denovoassembler/files/

Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.

Proper citation: Ray (RRID:SCR_001916) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/gatk/

A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

Proper citation: GATK (RRID:SCR_001876) Copy   

•   Source: SciCrunch Registry

http://www.agcol.arizona.edu/software/tcw/

Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.

Proper citation: TCW (RRID:SCR_001875) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

•   Source: SciCrunch Registry

http://www.myexperiment.org/

Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

Proper citation: myExperiment (RRID:SCR_001795) Copy   

•   Source: SciCrunch Registry

https://github.com/JialiUMassWengLab/TEMP

Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

Proper citation: TEMP (RRID:SCR_001788) Copy   

•   Source: SciCrunch Registry

https://github.com/nicolazzie/AffyPipe

An open-source software pipeline for Affymetrix Axiom genotyping workflow.

Proper citation: AffyPipe (RRID:SCR_002032) Copy   

•   Source: SciCrunch Registry

http://www.addgene.org

Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

Proper citation: Addgene (RRID:SCR_002037) Copy   

•   Source: SciCrunch Registry

https://github.com/adrlar/CanSNPer

Software that is a hierarchical genotype classifier of clonal pathogens.

Proper citation: CanSNPer (RRID:SCR_001980) Copy   

•   Source: SciCrunch Registry

http://www.candidagenome.org/

Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

Proper citation: Candida Genome Database (RRID:SCR_002036) Copy   

•   Source: SciCrunch Registry

http://biodev.extra.cea.fr/interoporc/

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

Proper citation: InteroPorc (RRID:SCR_002067) Copy   

•   Source: SciCrunch Registry

http://snver.sourceforge.net/

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Proper citation: SNVer (RRID:SCR_002061) Copy   

•   Source: SciCrunch Registry

http://polbase.neb.com/

Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software.

Proper citation: Polbase (RRID:SCR_006107) Copy   

•   Source: SciCrunch Registry

http://www.umd.be/BRCA1/

The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau.

Proper citation: UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) Copy   

•   Source: SciCrunch Registry

http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/

A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries.

Proper citation: PRED-GPCR (RRID:SCR_006196) Copy   

•   Source: SciCrunch Registry

http://www.mousebook.org/

Databases and portal to data and ordering mouse strains from MRC Harwell including mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies. The portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide added value information above and beyond what is available through other routes such as IMSR (International Mouse Stain Resource). MouseBook can be searched either using an intuitive Google-style free text search or using the Mammalian Phenotype Ontology (MP) tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual results lines from each catalog include information on gene, allele, chromosomal location and phenotype and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added enabling other sites to make their data directly available through MouseBook.

Proper citation: MouseBook (RRID:SCR_006358) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/IRanges/

Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible.

Proper citation: IRanges (RRID:SCR_006420) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna

A de novo assembly program targeting populations with high mutation rates.

Proper citation: VICUNA (RRID:SCR_006302) Copy   

•   Source: SciCrunch Registry