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http://genomeview.org/

A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute.

Proper citation: GenomeView (RRID:SCR_012968) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqminer/

Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).

Proper citation: seqMINER (RRID:SCR_013020) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mireap/

A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.

Proper citation: MIREAP (RRID:SCR_013025) Copy   

•   Source: SciCrunch Registry

http://www.lgm.upmc.fr/mirena/index.html

A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.

Proper citation: MIReNA (RRID:SCR_013024) Copy   

•   Source: SciCrunch Registry

https://mig.molbiol.ox.ac.uk/mig/

Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MIG (RRID:SCR_012972) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/brfss

The Behavioral Risk Factor Surveillance System (BRFSS) is a state-based system of health surveys that collects information on health risk behaviors, preventive health practices, and health care access primarily related to chronic disease and injury. For many states, the BRFSS is the only available source of timely, accurate data on health-related behaviors. BRFSS was established in 1984 by the Centers for Disease Control and Prevention (CDC); currently data are collected monthly in all 50 states, the District of Columbia, Puerto Rico, the U.S. Virgin Islands, and Guam. More than 350,000 adults are interviewed each year, making the BRFSS the largest telephone health survey in the world. States use BRFSS data to identify emerging health problems, establish and track health objectives, and develop and evaluate public health policies and programs. Many states also use BRFSS data to support health-related legislative efforts. Sponsors: This resource is supported by the Center for Disease Control. Keywords: Behavioral, Risk, Factor, Surveillance, System, Health, Disease, Chronic, Injury, Health, Behavior, Health,

Proper citation: Behavioral Risk Factor Surveillance System (RRID:SCR_012974) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/msa-edna/

Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.

Proper citation: EDNA (RRID:SCR_012981) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.

Proper citation: cn.mops (RRID:SCR_013036) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/samzip/

An encoding and decoding tool for Sequence Alignment/Map (SAM) files.

Proper citation: SAMZIP (RRID:SCR_012980) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://ccb.jhu.edu/software/tophat/index.shtml

Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.

Proper citation: TopHat (RRID:SCR_013035) Copy   

•   Source: SciCrunch Registry

http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry

http://sammate.sourceforge.net/

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.

Proper citation: SAMMate (RRID:SCR_013037) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/flexbar/

Flexible barcode and adapter removal for sequencing platforms.

Proper citation: Flexbar (RRID:SCR_013001) Copy   

•   Source: SciCrunch Registry

http://www.cochrane.org/reviews/clibintro.htm

Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors.

Proper citation: Cochrane Library (RRID:SCR_013000) Copy   

•   Source: SciCrunch Registry

http://rnai.dkfz.de

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

Proper citation: GenomeRNAi (RRID:SCR_013088) Copy   

•   Source: SciCrunch Registry

http://www.nccn.org/

A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers.

Proper citation: NCCN (RRID:SCR_012959) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/shrec-ec/

A bioinformatics tool for error correction of HTS read data.

Proper citation: SHREC (RRID:SCR_013009) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hictools/

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

Proper citation: hiCtools (RRID:SCR_013010) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/locas/

A software to assemble short reads of next generation sequencing technologies at low coverage.

Proper citation: LOCAS (RRID:SCR_013064) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/vdjfasta/?source=navbar

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires.

Proper citation: VDJFasta (RRID:SCR_013069) Copy   

•   Source: SciCrunch Registry