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https://github.com/AstraZeneca-NGS/VarDictJava
Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research.
Proper citation: VarDict (RRID:SCR_023658) Copy
Software to correct spelling and grammar.
Proper citation: Grammarly (RRID:SCR_023778) Copy
https://www.chemcomp.com/Products.htm
Drug discovery platform to integrate visualization, modeling and simulation in single package. Integrated computer aided molecular design platform.
Proper citation: Molecular Operating Environment (RRID:SCR_023932) Copy
Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response.
Proper citation: ChatGPT (RRID:SCR_023775) Copy
https://github.com/churchmanlab/genewalk
Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.
Proper citation: GeneWalk (RRID:SCR_023787) Copy
https://github.com/miRTop/mirtop
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Proper citation: mirtop (RRID:SCR_024116) Copy
https://sourceforge.net/projects/mpsqed/
Software tool for the design of multiplex pyrosequencing assays.
Proper citation: mPSQed (RRID:SCR_024118) Copy
http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.
Proper citation: SMILE (RRID:SCR_024119) Copy
https://github.com/biod/sambamba
Software tool to filter SAM file for soft and hard clipped alignments
Proper citation: samclip (RRID:SCR_024330) Copy
https://github.com/ekg/seqwish
Software tool for alignment to variation graph inducer.
Proper citation: seqwish (RRID:SCR_024332) Copy
http://technelysium.com.au/?page_id=13
Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Chromas (RRID:SCR_000598) Copy
https://github.com/rvaser/rampler
Standalone software for sampling genomic sequences.Supports two modes, random subsampling of sequencing data to desired depth and file splitting to desired size in bytes.
Proper citation: rampler (RRID:SCR_024207) Copy
https://github.com/cbrnr/sigviewer
Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.
Proper citation: sigviewer (RRID:SCR_024340) Copy
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Proper citation: pyomo (RRID:SCR_024188) Copy
http://sitplus.crea-si.com/index/index.html
Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.
Proper citation: sitplus (RRID:SCR_024344) Copy
https://www.artinis.com/oxysoft
Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements.
Proper citation: Artinis Medical Systems Oxysoft (RRID:SCR_024666) Copy
https://lifesciences.tecan.com/plate_readers/infinite_200_pro?p=tab--3
Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use.
Proper citation: Tecan i-Control (RRID:SCR_024562) Copy
https://github.com/STOmics/StereoCell_v2.0
Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries.
Proper citation: StereoCell v2.0 (RRID:SCR_024438) Copy
Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA.
Proper citation: tacg (RRID:SCR_024374) Copy
Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide.
Proper citation: WHONET (RRID:SCR_024495) Copy
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