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https://github.com/lh3/fermi-lite

Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.

Proper citation: fermi-lite (RRID:SCR_016112) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/Harmonizome/

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

Proper citation: Harmonizome (RRID:SCR_016176) Copy   

•   Source: SciCrunch Registry

https://github.com/sorgerlab/ashlar

Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.

Proper citation: ASHLAR (RRID:SCR_016266) Copy   

•   Source: SciCrunch Registry

https://github.com/BioDepot/BioDepot-workflow-builder

Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.

Proper citation: BioDepot-workflow-builder (RRID:SCR_017402) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/qtl2/versions/0.24

Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations.

Proper citation: R/qtl2 (RRID:SCR_018181) Copy   

•   Source: SciCrunch Registry

https://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

https://cluspro.bu.edu/

Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results.

Proper citation: ClusPro (RRID:SCR_018248) Copy   

•   Source: SciCrunch Registry

https://github.com/lanagarmire/lilikoi

Software tool as an R package for personalized pathway-based classification modeling using metabolomics data. Provides personalized pathway deregulation measurements (PDS scores) and offers a standardized classification model for biomarker prediction.

Proper citation: lilikoi (RRID:SCR_016361) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage

System designed for automated collection of images from a transmission electron microscope.

Proper citation: Leginon (RRID:SCR_016731) Copy   

•   Source: SciCrunch Registry

https://www.proteinmetrics.com/products/byonic/

Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type.

Proper citation: PMI-Byonic (RRID:SCR_016735) Copy   

•   Source: SciCrunch Registry

https://github.com/hakyimlab/PrediXcan

Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype.

Proper citation: PrediXcan (RRID:SCR_016739) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenSMFS/FRETBursts

Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.

Proper citation: FRETBursts (RRID:SCR_016898) Copy   

•   Source: SciCrunch Registry

https://github.com/gelles-brandeis/CoSMoS_Analysis

Software tools for analyzing co-localization single-molecule spectroscopy image data.

Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy   

•   Source: SciCrunch Registry

http://prosightlite.northwestern.edu/

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

Proper citation: ProSight Lite (RRID:SCR_016908) Copy   

•   Source: SciCrunch Registry

http://nrtdp.northwestern.edu/

Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.

Proper citation: National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://github.com/PathwayAnalysisPlatform/PathwayMatcher

Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.

Proper citation: PathwayMatcher (RRID:SCR_016759) Copy   

•   Source: SciCrunch Registry

https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst

Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.

Proper citation: Sashimiplot (RRID:SCR_016861) Copy   

•   Source: SciCrunch Registry

http://posa.sanfordburnham.org/fatcat-cgi/cgi/FSN/fsn.pl

Flexible Structural Neighborhood is a database of structural neighbors of proteins as seen by FATCAT - a flexible protein structure alignment program. The server accepts either a protein (PDB ID) or a domain (SCOP ID) as a query. For the former case, the server first displays the information of chains and domains of a given protein. Afterwards, users can retrieve similar structures for a domain (if domain information is available, i.e., the protein is collected by SCOP), or for a chain otherwise. The protein structure database we collected for similar structure search includes a representative set at 90% sequence identity of SCOP domains, and of up-to-date PDB entries that are not included in the latest release of SCOP.

Proper citation: FATCAT Flexible Structural Neighborhood (RRID:SCR_007665) Copy   

•   Source: SciCrunch Registry