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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
https://scicrunch.org/resolver/SCR_002250
THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.
Proper citation: OMICtools (RRID:SCR_002250) Copy
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.
Proper citation: bio.tools (RRID:SCR_014695) Copy
https://github.com/YangLab/CIRCexplorer
Software tool as a combined strategy to identify junction reads from back spliced exons and intron lariats. Computational pipeline to precisely identify junction reads from Circularized Exons. Used to identify circular RNAs (circRNAs and ciRNAs).
Proper citation: CIRCexplorer (RRID:SCR_016893) Copy
http://ccb.jhu.edu/software/hisat2/index.shtml
Graph-based alignment of next generation sequencing reads to a population of genomes.
Proper citation: HISAT2 (RRID:SCR_015530) Copy
Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins.
Proper citation: Johns Hopkins University; Maryland; USA (RRID:SCR_010247) Copy
Public research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of Maryland.
Proper citation: University of Maryland; Maryland; USA (RRID:SCR_011662) Copy
University of Washington is public research university in Seattle, Washington. Has university campuses in Seattle, Tacoma and Bothell, academic medical center and professional and continuing education programs.
Proper citation: University of Washington; Seattle; USA (RRID:SCR_011749) Copy
Public research university in the United States. Located in the city of Berkeley, it was founded in 1868 and serves as the flagship institution of the ten research universities affiliated with the University of California system. Berkeley ranks 5th internationally in the Academic Ranking of World Universities.
Proper citation: University of California at Berkeley; Berkeley; USA (RRID:SCR_011618) Copy
http://csbio.unc.edu/genescissors/
Software for detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.
Proper citation: GeneScissors (RRID:SCR_003146) Copy
https://github.com/howisonlab/softcite-dataset
Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.
Proper citation: SoftCite (RRID:SCR_024411) Copy
http://bowtie-bio.sourceforge.net/index.shtml
Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.
Proper citation: Bowtie (RRID:SCR_005476) Copy
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